Many of the so-called "new atheists" such as Dawkins and Hitchens take the naturalistic position that all religious belief can be reduced to a naturalistic system of chemical reactions in our brain. Although they tend to use this argument as a triumphant defense of atheism, Christian theologians respond with the point that atheism is also a set of chemical reactions. If ideas are invalidated merely because they depend on physical processes, no one group of ideas is proved more or less valid than another by that dependence.
More interesting is the claim that certain rather specific areas of the brain activate when religious people pray. Again, atheists argue that this shows prayer and other forms of religious belief to be able to be reduced to mere chemical reactions. But this doesn't really disprove that the object of prayer exists. Certain areas of sighted people's brain display chemical activity when they use their eyes. Just as we would not claim that the existence of a visual cortex proves light unreal, so too the existence of specific areas of the brain that are active in prayer or meditation does not prove the non-existence of the object of prayer.