Dan Gilgoff in US News & World Report says he's "mystified" at Obama's decision:
There are a couple of obvious reasons that Obama might want to skip a formal ceremony for the National Day of Prayer. The official task force for the event operates out of Focus on the Family, a longtime critic of Obama and of Democrats generally. It would have been awkward to have Focus's James Dobson on the White House grounds.
Then again, Obama has courted high-profile religious conservatives with more zeal than any other Democrat I can remember.
Another explanation for skipping an event: The Obama team might not have wanted to needle its generally secular base after catching so much flak over the Rick Warren inauguration appearance, expanding White House faith-based initiatives, and inviting conservative evangelical Tony Dungy onto its faith advisory council.
But Obama hasn't yielded to those pressures in the past.
My view: this kind of miscue is inevitable in the Obama Administration. It wasn't elected by Americans who respect things like National Days of Prayer - that is to say, the historic American nation - and has almost no contact with them. To quote me:
Although you wouldn’t know it by watching the coverage on election night, McCain very easily won the white vote in America in 2008. He won about 55% of it, a remarkable achievement really, considering the catastrophe of the Bush presidency...The 2008 exit polls have a lot of other fascinating details. They reveal these very deep and systematic divisions. So deep that you have to wonder whether the US really is still a nation with a common culture, or whether it has already become sort of a heterogeneous empire. One thing that fascinated me was the discovery that white Protestants still make up 42% of the electorate. 42% of the votes were cast by white Protestants still. And they voted 65% for McCain–overwhelmingly for McCain.
You have to wonder at this situation: white Protestants, of course, essentially invented the United States. As Phillip Roth says in one of his novels, [American Pastoral, p. 311]"Let’s face it, they are America." But they’ve completely lost control of the government.
Obama doesn’t have 43% of his appointees white Protestants, in fact I don’t think even 4% are white Protestants. So you have to ask yourself what’s going on here. How can the founding stock of the country have so completely lost control? They could reasonably regard the Obama administration as kind of an occupation government: a coalition of united minorities that succeeded in uniting the minorities and dividing the majority.