I feel the same way about shippers when it comes to my stuff. As long as people respect each other, it's fine even with the crackiest of ships.
As a creator I don't mind shipping. I like they invest energy into my comic. I also would be happy to make illustration for them on my Patreon about these non canon ships.
This far I only got one comment what bugged me what was like:
"If you don't do the ship I want, I'll call your comic queer-baiting." (It was phrased more passive aggressive but I don't remember exactly)
It made me think WOAH!
It's hard to imagine it came from pure love. :DDD It was more like a blackmail.
Personally, I enjoy people shipping my characters but I could see how if someone was commenting about a clearly non-canon ship every few pages or so that could just get annoying.. unless if it were like funny or something.
On the other hand, there are certainly times when the canon pairings are clearly not working and the work becomes frustrating to read. I'm going to use my favorite example here, which I've brought up before, of Seraph of the End (spoilers for anyone not up to date with recent chapters).
Summary
You have this relationship with Mika and Yuu that has been built up the entire f'ing story. They care for each other, support each other, need each other. They get physical with each other. Their relationship very clearly goes deeper than friendship.
And then you have the author's treatment of Shinoa. I love Shinoa's character but the way she has been written recently I feel has just been a disservice to her character. I still love the manga and everything, it's just this one thing with the character that literally came out of absolutely nowhere. Where you literally have other characters telling her directly "You love Yuu." And Shinoa's just like "no" and the readers are just like "um, where did this even happen?" because there's literally been zero romantic situations with the two of them. Like not even a hinting of it. And it has no relevance to the plot whatsoever. Like everything else that has happened could have easily happened without this "development".
It's just really weird and the only reason I can see them writing it this way is because there needs to be some sort of straight love for the protag at the end? I guess.
So in this case, I suppose I would be an unhappy shipper. But even so I wouldn't go around and out of my way to bombard the author with "Mika/Yuu!!11" Like, it's their story. If they want to make a totally incomprehensible relationship, then that's their thing, but also don't get upset if people are like "Hey. You've built up this huge Mika/Yuu thing and now you're suddenly pulling Yuu/Shinoa out of your ass."
I don't mean at all that people have to obey or respect shippers, but if you pull crap like that, then you're probably going to get some flak for it.
Basically, there isn't anything wrong with criticizing the bad writing of a ship or the betrayal of a ship. What is bad when it gets to the point as others mentioned where it's constant bombardment or goes into harassment territory.
I don't mind shipper (even crack ones), however I have a low tolerance for when they get aggressive. I have seen hardcore shippers get angry at creators for ignoring their ships. And creators getting annoyed at shippers may stem from people feeling entitled to having their ship in the series.
The weirdest annoyed shippers I've seen was people who shipped the two girls from the When Marnie Was There after seeing only the trailer. Then after watching the film, they learned how wildly inappropriate that was and got angry at the film.
I can say as a creator, it may also come from past experiences. I have no issue with shipping, but rather the actions of the reader about that shipping. Harmless shipping is fine, a few comments here or there about how it's cute or something, but when a creator is constantly bombarded or even attacked for a ship not happening, that's the issue. (Also, creators can't tell when people are being sarcastic through a comment. I've read some comments that seem downright cruel, only for them later to come across as joking. It's difficult to tell what someone REALLY means, but that's a whole other topic.)
As some mentioned, it's a few bad eggs that ruin the experience. Unfortunately, those past experiences can lead to many creators just tensing up at the idea of it. I had that happen to me when someone read my story, back when I didn't have much of a fanbase, and started harassing me to the point that I was crying for days on end. I couldn't get on my Wattpad account without some form of aggression from this person that I ended up muting for my own safety, only for them to make another account to comment on every single chapter again; about 200 comments that you simply can't avoid seeing even when you try. They were so angry about their ship not happening and so hateful of a particular character that I lost all joy of writing. Eventually I reported them and it stopped, but to this day I definitely tense up when I see ships that aren't the main couple in my comments, especially since I do have a much wider audience now. The paranoia is there even when I know most are all in good fun. I'm still working on this, but I won't even read the comments of that particular story anymore.
Again, it's the bad eggs that ruin it for everyone else. I've had some people ship my characters. I try to ignore those comments and let them have their fun, unless it does actually make me uncomfortable lol then I may ask them to take their discussions to private messaging or something.
EDIT: Creators shouldn't be mean to the readers though because they don't like shipping. I think it's fine to discuss, perhaps let the reader know what is making you uncomfortable and hopefully negate it from happening again while also letting them continue to enjoy their ship.
A bit unrelated to the topic, but I'm really sorry that you had to go through that.
It sounds really scary. 
Hope you're feeling a lot better now though 
Thank you. Luckily, I haven't heard from that person again (unless they made another account and I don't know it.) I'm much better now ^_^
I don't think that shippers should be hated, it's not bad to imagine a relationship, especially if you see the chemistry between characters. But there are some bad situations, sometimes the fault is on the creators playing with their audience, one example its Voltron, it was very controversial and manipulative and.... Really, really messy.
But well, the question is interesting because what I do if I get a ton of fans and I notice the shippers? I would consider their opinions and rewatch if the characters that they ship are showing good chemistry enough to put them in a relationship. But I don't want complains later if one of the characters has the end of his/her life just right at the corner, he/she will die anyway 
I don't think creators really hate shippers. What I think is that shippers tend to be so assertive that creators want to avoid resulting to fan service.
I can definitely agree on the Voltron comment;;;
As a creator, I don't think I'd mind people shipping my characters as long as they aren't trying to have me change the narrative to fit their ship? I have ships of my own in things so I totally understand but it's not always the duty of the creator to cater to what a percentage of the fandom wants? I'm trying to think of an example but it would be as if someone told Stephanie Meyer that she had to make Bella and Jacob be a couple and tried to force that even though that isn't the story she's created? (sorry for my outdated reference, I just wanted to give a hopefully well known example? lol)
I don't know guys, this. Plus rule 34 is when you know you've truly made it in your career. By my definition at least. =3=
I don't hate shippers when they stay on their own forums/groups and allow the creator to tell the story they've planned from the beginning. They can go insane and have all the wars they want, but leave that shit out from the comic itself.
Nothing takes me out of a story more than when the wall between fans and fanon, and the creator and canon starts to break. A ship that didn't exist but became popular all of a sudden starts to become canon because the creator either wants to do more fanservice (and become more popular I guess) or feels pressured to please their audience. This alters the whole story, possibly leading to retconning plotlines and all sorts of nonsense.
Readers see this, and in the worst case scenario the immersion is gone. They have to wonder what else is going to be changed by the small, but ferocious group of fans. It's no longer a coherent story, but a series of plot points dictated by forces outside the creator's control.
I think the issue with shippers from a creator perspective is less them discussing with other fans how they'd like a story to go or imagining alternative ways it could have gone through fanfic or fan art, and more that some of them seem to want to tell the creators directly how to make their story.
Like imagine you're making a cake, a delicious carrot cake and somebody you've never met comes up and says, "hey, you should make this a chocolate cake", and you say, "sorry, I actually really want to make a carrot cake", but they keep insisting, "NO. You're doing it wrong, nobody wants this carrot cake, a chocolate cake would be better." and you're like "But this is MY cake! I'm making the cake how I want to make it, I didn't even get out the ingredients for a chocolate cake! I don't know how to make a good chocolate cake!" and then it escalates to, "IF YOU DON'T MAKE IT A CHOCOLATE CAKE, YOU'RE A BAD BAKER! AND YOU'RE A BAD PERSON!" and you wonder how it got like this from your original innocent notion of "ooh, I think I'll make a tasty carrot cake!"
In most cases, it doesn't get that far, but it's just generally frustrating when you're making your own creative work, and usually as a solo creator this will be a labour of love made because you wanted to make it, not out of some corporate mandate, just purely "I think a comic/story like this would be cool and I want to make it" and suddenly somebody is telling you how to make it. Especially when on platforms like Tapas or Wattpad, there's really not much preventing literally anyone from making their own work that does have the kind of ship they're interested in instead of trying to backseat drive somebody else just because they already put in the work to build an audience. If it's a big corporate production, I kind of understand more, since marginalised people are often locked out of making their own works in print or for TV etc. So lack of representation, hetero-normativity and queerbaiting is a legitimate and frustrating issue there and it may feel like the only way to have a voice on the matter. Still, some fans have definitely taken this too far.
tl;dr, most small creators are just doing it out of love and you can always make your own thing, so if you're not giving them objective critique they actually asked for, let them enjoy making what they want to make, even if you'd prefer if the pairings were different.
I have no problem with shippers, in my comic there is not much to be shipped though XD
(well maybe in my other comic but I still have to update it lol)
I didn't even know that shipper was a thing LOLOL I guess my comic3 still didn't had the opportunity to attract shippers but I'll get back to this soon I know what it feels.
Oh BOI, as a new creator here in tapas (and a notorious multishipper myself 
) I would go over the moon and find it extremely entertaining to have readers who ship my characters. Even if they saw subtext where there wasn't none.
I often joke with my IRL friends, who are familiar with my story and script, about "who might end up shipped with who" if my story had a big enough fanbase and I find it crazy funny.
It's all in good fun in my book. As long as people aren't trying to push their headcanons as canon or pressure the creator or fellow readers into liking or disliking a ship then it's almost like my favourite thing. Crack ships and all. I just love all of it. 
Man, as someone who's been part of fandoms, even imagining shippers for my very own story sounds so surreal (especially since it isn't even the romance genre lmao). To me it would just be a sign of reader engagement and that I've managed to get people invested which is what I've always dreamed of. 
(But I am aware of situations where shippers and creators have gone too far with their behavior ofc)
While I've never personally seen this happen with other creators in Tapas (the most I've seen is just joking around), I AM someone who engages in fandom regularly. For fuck's sake, I used to be a Voltron fan, and if you've been on the internet since 2018, you'd, uh, know how rabid Voltron fans got. Now the fandom's mostly dead. Thank god.
Now, I have a PhD in Fandom Culture and - no, no I don't. I just decided to keep my Tumblr account after the Great Porn Purge of 2017 and I decided for whatever masochistic reason, I decided to keep using it.
With that in mind, I agree with darthmongoose, I think it's because some shippers will complain about the direction of the story if it doesn't cater to the "favorite ship". The most rabid of which will DIRECTLY THREATEN the creators of said work to make x ship canon (again drawing back to the Voltron fandom, this is something that actually happened - someone threatened to leak an entire season or if they don't make klance canon). I've even seen shows and stories where the creators bent over backwards to make the most popular ship in the fandom canon to please, well, the fandom. Though, I guess that boils down to the creator/s' willpower than the fans.
Obviously, not all shippers like that, but a vocal minority will often be the image of a group rather than the quiet majority. Or something like that.
Shipping is for fun and it isn't something to be taken seriously, lmao. As a creator, I would love it if my readers began shipping characters in my comics because it means they liked the comic a lot and paid enough attention to the story to begin looking for subtext there. It's nice.
