Just saw the movie/documentary with some friends. A few thoughts...
Bill Maher is a smart man and surprisely did not offend me as expected. He was more honest than most and came from a position of doubt and "I don't know" about religion.
It seems to me he asked some tough questions any normal, thinking human being would ask. Questions about talking snakes?, living in a big fish for 3 days?, virgin birth?, similar religious myths?, homosexuality in nature?, prosperity of the religious not helping the poor? and end times violence???
Bill is not the only one with questions of doubt. I think a more helpful posture to have is one of seeking truth with him instead of arguing truth against him.
Some principles...
1. Drop the Fundamentalism. Admit that we have doubts too. Go beyond the I'm right and you're wrong debate posture. Seek truth, don't defend it militantly.
2. Deepen our Folk Religion. Give Biblical answers rather than bumper stickers. Read the whole counsel of God, engage in challenging dialogue and develop a sound theology.
3. Depend on Revelation. Truth is greater than the western mindset of the scientific method. God reveals himself in a Person not in arguments of doctrines, tenets or practices.
After Jesus is raised from the dead, we find this verse in Matthew 28:17, "When they saw him, they worshipped him; but some doubted".