I have definitely seen unreasonable reactions to trans characters. As a nonbinary person, I've had to think seriously about whether to represent elements of my own identity that might get me called transphobic, but your phrasing seems very dismissive of people who might be upset. Even though you ask if it's good, you also talk about "people getting called bigoted for having a different opinion", which makes it sound like your focus is a bit more on how you want to be seen than how you want trans readers to feel. Don't think about "is it transphobic". There's no objective answer to that, and us trans people aren't a hivemind. Instead think "how might this make trans people feel, and am I willing to accept the consequences for the people this might hurt".
For some personal examples on both decisions
Summary
I identify as both nonbinary and lesbian. Some people find this confusing and contradictory, offensive to trans people, or offensive to lesbians. I can explain why the term makes sense for my experience, but that doesn't mean readers will feel the same way. When I chose to make the lead of Left to Rot a nonbinary lesbian, I was really worried about the response, but I decided not portraying an identity, especially one I shared, because I was afraid of backlash, was cowardly. I didn't actually feel I was telling a hurtful story, I just didn't want mean comments.
On the other hand, I like skeevy characters, and I'm gay. If I'm writing something the world will never see, I'm happy to fill it up with skeevy lesbians. But there is a long, nasty history of The Predatory Lesbian in media, so I don't write that for public stories. It's not just about getting 'Called Out', it's about
A) Knowing I could really hurt lesbian readers, or validate the worldview of homophobic readers
B) I would no longer be telling the story I wanted to tell. Being a writer means knowing connotations. Readers know what a stormy night means and what a pair of doves mean. If I key into that trope, readers would not see the story I was trying to tell.
There are bad faith readers, but LGBT+ opinions are very rarely "you can never write a flawed LGBT+ person". It is specifically that LGBT people, especially trans people, have a long history of being seen as dangerous, predatory, and immoral, and cast in villain roles. Even as we've moved past some attitudes, there can be a tendency to push characters towards that role. (Think of all the scary male villains with effeminate gestures, or who creep on the male lead) Because of that there's two things that can be very important
- Do the research. Learn what tropes are hurtful and why.
- Show LGBT people in other roles. You can say the character's villiany and trans-ness are totally unrelated, but it still means the only trans person in your story is a villain.
On the flipside, if you're only thinking about Doing It Right, it can be easy to flip the other direction and be so afraid of Doing Representation Wrong you either close down and only write what feels 'safe' or end up with something totally toothless where only white, cis, straight men are written as complex, interesting people because the author is so worried about doing it wrong.
This isn't the main take in the thread, and sounds a bit harsh, but I'd say maybe wait a bit on writing a trans villain. I don't think it's something you can never do, but the fact that you're asking "are trans villains bad, I don't want to get called out" rather than "why do trans villains upset people, and what do you think is important to understand before writing a trans villain" makes me think you should give it some time.
One more thing. If the character's villainy is unrelated to their trans-ness, as most people in this thread advise, why have you chosen this character to be trans? Did you consider making the hero trans?
There are plenty of answers to this that are totally valid reasons to make a character trans, but sitting with questions like this can really help you either see bad patterns in your writing or force you to articulate why it's important to the story you want to tell.