1. Bill Maher needs to figure out how groom his hair so it doesn't look like greasy seaweed. Seriously, on the big screen it's really an uncomfortable distraction.
2. All of the interviews were very dishonestly edited. Several times I saw cuts after something Maher said to a reaction shot of the interviewee, where the interviewee wasn't reacting to what Maher said. Any time there's an edit like that, it's just to make the interviewee look like an idiot.
3. You can always have the last word if you're editing the interview. You can also cut out any part where the interviewee makes a reasonable rebuttal to Maher's premise.
4. His whole thesis in this movie -- that religion is bad -- can be refuted thusly:
Everyone from Paul of Tarsus to Gödel has shown that all knowledge is incomplete, that all models of the universe are provisional. Religious people have their imperfect models of the universe, and atheists have theirs. You can make an effective argument (as Maher does, up to a point) that a scientific empericism is closer to describing the 'real world' than religious faith.
But you can't make an effective argument that an atheistic or agnostic world view is 'better' -- for two reasons: 1) Assuming that you can objectively judge the outcomes of decisions, in both the religous and secular can you argue that one is 'better'? 2) Can you even judge anything objectively?
This is a functional argument for religious faith -- even if some of the things you believe are silly, you may in fact be a better person for your faith. The same thing goes for atheists -- you can argue atheism meaning there is no a priori morality. Atheists can choose to be go wild on the world, since nothing has any particular meaning. Or you can work from human tradition, common sense, and come to a human idea of moralty.
But what you can't say, scientifically, is "those people over there are nuts." Which more or less is what Maher's movie is all about. You don't know enough about the universe to make that judgement!