A redated post.
This is from my response to the Carrier-Wanchick debate.
Carrier relied on an argument from displacement, but it is the nature of science not to look for supernatural causes, or if so, to accept them as a last resort. It is like saying that the $100 bill you lost at the beach must have been stolen because after scouring the area with a metal detector, you didn't find it. Science is extremely good at telling us some things we need to know; there are other things it is not so good at, and it is far from proven that we ought to make science the measure of all things.
Jan 1, 2011 addendum: Methodological naturalism in the sciences actually weakens the argument for atheism based on science. The only way scientific evidence could possibly undermine religious belief would be if scientific evidence could have gone the other way and confirmed religious belief.