This phenomenon is certainly a problem - the SU fandom bullying another fan into attempting suicide is possibly the most extreme example I've heard of (outside of things like, you know, Gamergate), but it happens every now and then and it bothers me. I've yet to be subjected to it, despite having quite a few readers and a social media presence, and I hope it doesn't happen.
To be clear, 99% of fans are genuine fans - people who, even though they might sometimes be disappointed in your story, realise that it's a story, and don't decide to personally attack you for it. But that 1% is definitely annoying.
I think it comes hand in hand with the rise in access to creators. Before the rise of social media, the only way to get in touch with a creator was via email - and before that, via fan-letters. Now, you can just find them on Twitter and talk directly to them. It breeds a sense of familiarity - which is positive in some ways, but also has some negative consequences. Just because a creator is polite to you online doesn't mean you're friends, and it DEFINITELY doesn't mean you have the rights to demand the creator to do things to suit you specifically.
Discussion and critique of works that employ harmful stereotypes? Yes, do that as much as you can. Whine and threaten a creator to get them change their story to what YOU want? DON'T.
.... One reason I think it happens more often with webcomic creators and the creators of tv-shows and such is due to the serial nature of the medium. We don't deliver a complete story in one single release; we release it piece by piece, and in between those releases, people have the time to speculate and decide on what THEY would like to happen - and emotionally invest themselves in those possibilities. I do it too! I just don't whine and complain when those possibilities fail to materialise.
It kind of ties into the whole issue of condemnation culture as well; you know, the kind of vaguely aware social-justice-crusading-slash-witch-hunt that rolls around on Tumblr regularly, where fans decide that a certain character or storyline is "problematic" and want it gone, without thinking any further about it. And I don't mean campaigns against using harmful racist stereotypes - I mean the kind of crusade that takes aim at a character for not being 100% perfect sweetness and light and goes into a frothing rage to get rid of it.
It's a fundamental misunderstanding of storytelling as a concept. You aren't meant to love every character or approve of what they do, and some bad things do need to happen to the protagonist or there will be no story - and characters doing something bad doesn't mean the author endorses that bad thing.
I am 100% in favour of a healthy critique of the things you enjoy, and even of the things you don't, but there is a UNIVERSE of difference between "I dislike this and think that it's bad because [x]" and "You did a thing I don't like, I will now bully you into committing suicide". Healthy critique is necessary for creators to grow - frothing rage-crusades are not.