Like a cross between PJ O'Rourke and Richard Dawkins, he seeks out a variety of the faithful and asks them to explain precisely how their beliefs tally with science, history, statistical probability, etc. He's funny with it – I especially enjoyed his meeting with the actor playing Jesus at a Christian theme park – although, as with most contrarians, he eventually becomes rather hectoring. You also begin to notice that his interview subjects tend towards the weird – a Holocaust-denying rabbi, a maverick priest outside the Vatican, a blinged-up evangelical minister who used to sing with the Blue Notes – and aren't exactly trustworthy representatives of God's message.
It's pretty easy to take the piss out of religious kitsch, as Maher does. It would have been more instructive (if less chucklesome) if he'd risked an argument with an accredited theologian, or a Christian aid worker, or one of the millions of ordinary people who worship at a church. Not all of them are nutters. But then such an admission might have spiked his comic guns.