he's actually anti all religion, not just Islam.

That's not the problem. I'm against all organised religion too, including Islam. The problem with Maher is that he treats everyone who's Arab or otherwise culturally Muslim as equivalent to the worst fundamentalist preachers and also that he platforms and promotes some of the worst islamophobes from the far right, more of whom are Christian bigots than atheist ones.

TL;DR: it's not the opposition to the religion, it's the bigotry and the hypocrisy.