Obama said:

We know that our patchwork heritage is a strength, not a weakness. We are a nation of Christians and Muslims, Jews and Hindus — and nonbelievers.

Decius wrote:

I believe that is the first respectful public reference to atheism by an American President. Reply if you know of another example.

There seem to be examples in the historical record, with the exact number depending on your specific criteria for "respectful" and "public." I presume you meant "public" in the sense of a public utterance, not a private letter that is now part of the public record.

There are statements attributed to Thomas Jefferson:

I concur with you strictly in your opinion of the comparative merits of atheism and demonism, and really see nothing but the latter in the being worshipped by many who think themselves Christians.

-Thomas Jefferson, letter to Richard Price, Jan. 8, 1789 (Richard Price had written to TJ on Oct. 26. about the harm done by religion and wrote "Would not Society be better without Such religions? Is Atheism less pernicious than Demonism?")

And also to Teddy Roosevelt:

To discriminate against a thoroughly upright citizen because he belongs to some particular church, or because, like Abraham Lincoln, he has not avowed his allegiance to any church, is an outrage against that liberty of conscience which is one of the foundations of American life.

RE: Obama's Inaugural Address