Strangely enough in almost every history of rational thought or atheism there is one person who almost everyone starts with. Epicurus. While I think Epicurus is a great philosopher and one of the first historically recorded atheist thinkers (though he might have not been an atheist...wait till part 2!). He is not, sadly, the father of rational inquiry. The man who takes that place is Democritus.
His ideas in epistemology though, ah now that reserves him the place in the history book of rational thought. Democritus's idea was that we had only a subjective view on an objective world. While we will never be sure that what we observes is actually real, our thoughts and logic can be used to determine what is real.
While I must disagree with his conclusion on logic (concluding that logic is proscriptive rather then descriptive is a no no!). He still holds an important place in the history of rational thinking. Until this time no one had actually pointed out that the world was objective and that our experience of it was subjective. This seems obvious to us now but even in that time people had argued, and apparently convincingly so, that reality itself could be subjective.
Democritus truly placed the foundational stone of rational thought, without this first steady(ish) concept to work from no skeptical rational inquiry can proceed.