I think, similar to other comedians like Stone/Parker, Key&Peele, Seth McFarlane, Ricky Gervais, etc, Chapelle has the reputation of an equal opportunity jokester, so I think it's kind of silly to get selectively pissed at individual insults.
If bits stop going over well with audiences, they will get phased out of the act. That's how comedy works. If you go to an R-rated show with the expectation that everything you hold sacred will only be mentioned in a positive light, you should probably find another form of entertainment.
Obviously trans people are near the bottom rung in terms of groups that society respects enough not to insult to their faces. But I don't think a blanket ban on trans jokes is the answer.
There can be and have been funny jokes about black people, from black/white/hispanic/asian comedians. Some of them play up obvious stereotypes. You pretty much have to judge a joke in the context of who's saying it, what it says, and how playful the tone is, you can't blanket say "you can never make fun of black people's diets or music or naming conventions."
It's context that makes a university blackface/gangsta party or the Redskins logo offensive and racist, not just the fact that black people are the butt of a joke.