True. No is perfect. And it has indeed been Stapp's struggles that have given much material create songs with. But to get back to the original question, Stapp wouldn't be so hated if he didn't look like a walking contradiction. Don't get me wrong, I love his music, and fully support his ambitions. Moreover, Stapp's behavior isn't exactly new to the world of rock. But his music is so rich and full of beautiful and meaningful messages, and he isn't afraid to say that his music is supposed to be meaningful, and to teach a lesson. But then, he turns around and does all sorts of outrageous behavior, and doesn't seem to actually live according to the values that are espoused in his music. He seems to talk the talk, but not walk the walk, and I think that this annoys lots of people who might otherwise have no problem with him.
And then of course, there was the whole controversy around the actual music, the supposed Christian messages, and the backlash against post-grunge. These probably just compounded things.