Michael Newdow (who sued to have the words "under God" deleted from the Pledge) and others have filed suit to stop the prayer and other religious expression at the inauguration. They claim it's exclusionary to others who don't share religious views and is restricted by the First Amendment of the Constitution. I heard Michael Newdow claim that Obama's freedom of expression stops when he becomes president.
It's always odd how these sorts of law suits actually turn the First Amendment on its head. Freedom of expression was pointedly intended for the public square, political or religious. And the oath of office doesn't require the president to renounce his Constitutional rights. In fact, that would be a contradiction. The Constitution specifies rights that are God-given, unalienable, that the government cannot restrict. And if the Constitution then offered an oath restricting those rights, it would be something of a quandary, wouldn't it?
The government is not to establish a religion - that's the separation of so-called "church and state." That is, making an official church and/or requiring a religious confession. A prayer at a public event does no such thing and is, obviously, voluntary. No one is compelled to participate. And these kinds of public religious expressions are in complete keeping with the Founders' own practices, even more tame. The author of the "church and state" phrase so often snatched out of context, Thomas Jefferson, approved of and participated in church services held at the capitol building.
The point of religious pluralism and tolerance is where we meet in the public square, not to drive religious expression into the private realm. It's time for these atheists to be tolerant as others practice their civil liberties.