No doubt the founding fathers believed in god, and religious freedom. Most of their families had left Europe to seek religious freedom. They wrote into the laws of the land that no one religion would be "the religion" and guarenteed religious freedom. Reading the Federalist Papers and other documents from the time strongly indicate that was their intentions. Therefore our laws are based on religious morals and principles. Fortunatly those beliefs are sound for anyone, believer or not. (don't murder, steal, covet, slander, etc.) Most religions are founded on those principles so I have no problems with people that accept and adhere to the principles regardless of religion or not. Where we get twisted off in the wind is when non believers and believers start debating the finer issues not specifically covered in the ten commandments (christians) or rules for muslims (from the Koran) as evidenced by the abortion debate. When does life begin, therefore when is it murder which, most religions specifically prohibit.
Now to answer the original question, would I support an athiest for President. Being a Christian myself probably not, however if they were the lesser of two evils and I agreed with them on the non social issues (taxes, defense, etc.) I might. But until the way we change the way we pick our leader it probably will never be an issue. Without the support of one of the two major parties you will never be elected. And that support comes at a huge price. Comprimise, comprimise, comprimise! You have to pay your dues to the party, serve your time, scratch the right backs and play the right games to even be given the chance to run.
Finally, as an interesting aside when Americans were polled as to whether or not they though they were going to heaven when they died over 90% said yes. Does that mean that over 90% of Americans are religious? Heck no it just means that over 90% of Americans think they ought to hedge their bet, just in case.