He actually does discuss things like radical fascism, and outright calls them 'basically religion.' (That's from memory, I'd have to check to get you an exact quote.) But he does stress that these things, just like religion, deal in absolutes which are held as universal despite being mandated by humans. From this film, anyway, I get the impression that Maher is after the absolutism, the determinism, the literalism. Maher is after those instances where religion, or any other ideology is not used to enrich lives, but to control them.

The problem isn't intolerance, it's allowing behavior to be tolerated under the name of religion that would not be tolerated anywhere else, under any other circumstances. After all, tolerance oly works so far; when tolerance requires that intolerance be tolerated... well, that's a bit of a problem, no?