The brain’s “God-shaped hole,” as it has been called, is a logical necessity of the pattern-recognising neurology which is the basis of our ability to reason.
An atheist can claim that belief in the God of Abraham and Moses is problematic based on theodicy, but he can’t argue that the belief in some sort of God underpinning the orderly rational universe of some sort is irrational, since the very operation of reason hinges on the orderly universe which, by evolutionary logic, created it.
In short, if belief in God has been naturally selected, it cannot be rejected as illogical by someone who believes in evolution.