The President is allowed to be whatever he wants to be, be it Atheist, Pastafarian, or just wears a tinfoil hat so the martians don't brainscan him.
However, in practice, we haven't yet had a non-Christian President simply because a large portion of the population would not vote for someone who was not Christian. They don't have to be a regular practitioner that goes to church every Sunday, and most of the country just doesn't care, but a large enough slice of the population (especially in the important swing states) just would not vote for someone if they were Jewish, or God forbid, Muslim. Atheist would actually probably be more likely than Muslim to win right now.