It is meant to be funny and to make us think. He has a rather Michael Moore-esque approach to the film meaning he tends to make fun of those he disagrees with in order to prove his point. Perhaps right-wing Conservatives do the same thing in their documentaries. I wouldn't know. As a bleeding heart liberal I tend to stick with my own kind.
(For full disclosure I will add that I do believe in God. I'm not so sure about religion. I was brought up Catholic but have questioned my faith on and off through the years, most recently when a colleague said she had a hard time belonging to a religion that did not accept her as a full member.)
The movie was pretty funny but I don't feel that Mr. Mahr made his point well. For one thing, he kept interrupting the person with whom he was speaking. He'd ask a question and before the other guy could respond, Mr. Mahr would be off on a tangent. The other guy, usually a religious figure, would keep saying, "Let me finish." But Mr. Mahr seemed to full of his own witticisms to let anyone make their case.
He did enlighten us (or at least me) on several interesting topics including the Egyptian God Horus who was also supposedly born to a virgin, performed miracles, rose from the dead and predated Jesus by 1500 years.
While it was a pretty funny movie and Mr. Mahr is extremely intelligent, I feel that the best part of the movie came in his summation. He delivered a monologue at the end of the film that I feel truly drove his point home in a way that the film did not. I can't re-print it all here but I've a few quotes. His entire summation can be found on the quotes page of IMDB.
"Faith means making a virtue out of not thinking."
"Religion is dangerous because it makes human beings who don't have all the
answers think that they do."
"And, anyone who tells you they know, they just know what happens when you
die, I promise you they do not. How can I be so sure? Because I
don't know and you do not possess mental powers that I do not."
"The only appropriate attitude for man to have about the big questions is not
the arrogant certitude that is the hallmark of religion, but doubt. Doubt
is humble, and that's what man needs to be considering that human history is
just a litany of getting shit dead wrong."