Some people seem to dislike him simply because he is fat. Some people hold his lesbian past against him, although I don't see the logic of that. Some people complain that he seeks too much publicity, although I have mixed feelings about this myself. I don't know much about his lesbian activist stage, but he would have had a hard time transitioning quietly, so why not make the best of it? Some people pick apart his "female" characteristics and say he's not masculine enough. Maybe he isn't particularly masculine, but they can do this because they know he's trans and they have access to old footage of him.
And some people complain that he shouldn't try to speak for all trans men. I haven't seen enough of him to know whether he really does this. I do know that a couple of things that Bono said were quoted out of context, without his little disclaimer that he was speaking for himself. I don't remember the specific passages now, but some of it came from Letterman. Stuff like how HE looks at being trans, etc. And then he said one or two questionable things that had no appropriate context that I recall. But as I said, I'm not knowledgeable about all things Bono, and I don't want to be.
With all of that said, I don't think he comes across as particularly articulate, introspective, or enlightened. So, yeah, I'd rather have a few representatives other than Buck Angel and Chaz and even Lucas Silveira. But they will come in time, and I'm sure as heck not going to put MYself out there.