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.

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

Update:
Although the Obama team has completely upgraded Whitehouse.gov, Google still has the old version cached, which includes the only reference Google knows to this exchange with Bush 43 at an "Ask President Bush" event:

Q ... Mr. President, as a member of the local clergy of this city, I'm appalled at the different lengths of political correctness that has affected religious rights in Canada, Australia, France, and other European nations. Laws are being passed to limit offensive speech. If reelected, what will your administration do to the rights -- to help the rights of conservative Christians so that courts in America can't limit our free speech when it comes to offensive speech toward different groups?

THE PRESIDENT: Look, here's the thing. Freedom to speak is a valuable part of our country. And a President has got to protect that. People ought to be allowed to speak the way you want to speak. But there are limits. And it is very important for our society to work with those that push the limits without abridging anybody else's freedom to speak.

Let me talk about freedom of religion, as well, which is an incredibly important part of our society. My job as the President is to make sure -- this may get to your question, by the way, besides speech -- an incredibly important part about what you're asking is, can people worship freely, as well. Yes. That's the part of the job of the President, is to make sure that people can worship any way they want, any way they want. And they can choose any religion they want. Or they can choose no religion. You see, you're just as big a patriot -- as good a patriot as the next fellow if you choose not to worship. It's your choice to make. And the freedom of this country is that you can choose to do any way you want. And it's important that we keep that -- that freedom real and intact.

The move from atheism to patriotism seems to evoke this comment that Bush 41 made:

I don't know that atheists should be considered as citizens, nor should they be considered patriots. This is one nation under God.

There is some question as to whether or not Bush 41 actually said that, the Whitehouse never denied it, it has been widely quoted for years, and it certainly molded my impression of how the establishment in this country views atheism.

Obama's Inaugural Address: The Full Text -- TIME