Michael Newdow failed in an attempt to block the saying of a prayer at President Bush's inauguration. The judge in an impressively comprehensive opinion had two main points: (1) an injunction against the President overall is a high test to meet, one hindered in this case by another similar lawsuit by Newdow that was rejected and (2) the Supremes upheld legislative prayer because of its long history from the time of the First Congress, and this ceremony has a similar heritage.
As an original manner, Newdow might have a case following traditional establishment principles, but this sort of thing is treated separately. This is a sound reading of questionable precedent as suggested by a law review article cited by the opinion:
There is perhaps no more of a defining moment in the American democracy than the inauguration of a new President. Inaugural prayers are quite different from legislative prayers in that they are patently intended for all Americans. ... Inaugural prayer violates the endorsement test's effect prong for the very same reasons legislative prayer does because it too endorses religion over nonreligion and Christianity over other religions. If the purpose of inaugural prayer is to solemnize the seriousness of the occasion, surely this function can be achieved equally effectively through nonreligious means. Consequently, inaugural prayer is unconstitutional.
-- Steven B. Epstein
The inauguration is just one of many instances of ceremonial deism in this country in which God is deemed an essential part of public ceremonies with governmental or quasi-governmental bodies formulating actually how it is done. Acceptable or not in this individual instance, at some point a troubling line is crossed. For a discussion about how this sentiment might invade our science class rooms, see this discussion.
On the other hand, there is always the philosophy that we really should not think too hard. This is the approach taken by President Bush, who argued:
[T]he public's decision to reelect him was a ratification of his approach toward Iraq and that there was no reason to hold any administration officials accountable for mistakes or misjudgments in prewar planning or managing the violent aftermath.
"We had an accountability moment, and that's called the 2004 elections," Bush said in an interview with The Washington Post. "The American people listened to different assessments made about what was taking place in Iraq, and they looked at the two candidates, and chose me."
He also noted that we haven't caught Bin Laden yet because "he's hiding" but like O.J. we are still "on the hunt." Likewise "on a complicated matter such as removing a dictator from power and trying to help achieve democracy, sometimes the unexpected will happen, both good and bad." [Not really in this case, since what was happening was mostly predicted by many people.] And, other pearls of wisdom.
The sad thing is that he almost has a point. The public should have known him enough to realize that voting his re-election would be taken as reaffirmation of all that was done in the first four years. This is akin, by the way, of not divorcing your spouse being taken to mean that said spouse did nothing wrong or worth reforming. Life just doesn't work that way when we deal with rational people who actually have a willingness to show some humility and ability to learn from experience.
This leads back to the opening issue in one of two ways. It is either sacrilegious (like a doctor taking part in a death sentence) to bless the inauguration with the presence of clergy. Or, we need as much help as we can get ... those who are worried about such things as what message is being sent etc. are not a big concern of this administration anyway, right? They lost on November 2.