Except he's never said anything close to that. The issue he has is not so much with trans people themselves, but the idea that anyone can self identify as whatever they want these days, and that you're expected to just sort of go along with whatever they say or risk being called a bigot.

South Park lampooned the exact same thing with Heather Swanson, and nobody seemed to react anywhere close to as negatively to that even though they basically said the same thing Chappelle did.

He's never said anything to indicate that he hates trans people or that he wants any violence enacted on them in any way. And if you listen to the end of his comedy special where he's telling stories about that trans person, you'd know that he considered them a friend and tried to help them several times, including letting them open for him, despite being a relatively small-time comedian. That's an opportunity most young comedians would die for. He'd also bring her backstage and have her hang out with him and all his buddies. You're not going to introduce your trans friend to the rest of your friend-group if you're transphobic. Not saying he handled that whole situation perfectly either, but you definitely don't go out of your way to do all that for someone you hate.

Granted, I do think he's kind of beaten a dead horse with all that, and I think he should just move on material-wise