It might be an unpopular opinion, but a lot of queer folk are as clueless about Christianity (and religion more broadly) as religious people are about transgenderism (and LGBT more broadly).
Christianity, and other religions, are considerably more complex than people who read nothing about them think. Just like trans people make a lot more sense when you read about it at least a little bit. Both sides are guilty of being incredibly ignorant and uninformed.
That said, however, only one of those sides is actively pursuing removal of the other one from existence. So there's that.
Also, remember that the Church has little to do with the religion itself. Hell, the Church is literally the people who crucified Jesus. It doesn't get more ironic than that. The Church fulfills the same function for religion as the government does for society. You can fill in the rest yourself.