One of the issues where religious believers have the least sympathy for atheists and church/state separation is the Pledge of Allegiance. This isn't hard to understand because it's one of the most prominent forms of religious privilege, but it's also one of the starkest ways in which anti-atheist bigotry is both promoted and accepted in American society. Every day children recite a religious oath which devalues the patriotism and equality of atheists. Barack Obama supports this completely.
In his "Call to Renewal" Keynote Address of June 28, 2006, Barack Obama demonstrated just how little he cares about the experiences of atheists or how government promotes bigotry against atheists:
It is doubtful that children reciting the Pledge of Allegiance feel oppressed or brainwashed as a consequence of muttering the phrase 'under God.' I didn't.
What is really doubtful is whether Barack Obama has ever stopped to seriously consider what it must be like for atheists or what effect it might have on other children to take a religious oath as part of the Pledge of Allegiance. At least, that's the most generous interpretation because if he has seriously thought about it and came to this conclusion, it would probably follow that he personally shares in that anti-atheist bigotry.
I'm sure Barack Obana didn't have any problems reciting a religious oath with the words "under God." Even though he was raised in a generally secular household, there is no evidence that he was ever an atheist himself. Given the religious background of his family, his theism was presumably along the lines of traditional western monotheism. In that case, "under God" would have been relatively natural. Indeed, since it reflected the beliefs and attitudes he was raised with, it's unlikely he ever gave it a second though - making this a perfect example of how a nonconscious ideology works.
For people who don't implicitly share the assumptions of traditional monotheism, the Pledge of Allegidance looks very different. People reciting it are expected to repeat a phrase which doesn’t correspond with any of their own assumptions, beliefs, traditions, or practices. Because it is so contrary to everything else they believe, it stands out prominently - and serves as a stark reminder that one is part of a second-class group.
Imagine, for a moment, that the religious oath in the Pledge of Allegiance read "under Jesus" instead of "under God." Would it make sense for a Christian like Barack Obama to inform Jews and Muslims that they surely don't feel oppressed as a consequence of their classmates swearing an oath to Jesus every morning? Would it make sense to insist that swearing an oath to Jesus isn't a serious or important violation of church/state separation?
We can see the same problems if we remove the issue from the realm of religion, too. Imagine if the Pledge of Allegiance said "one White Nation, under God." Do you think that Barack Obama, a black man, would deny that blacks should or do feel oppressed as a consequence of their classmates swearing an oath to White Supremacy every morning? Would it make sense to say that swearing an oath to White Supremacy isn't a serious or important generator of racist bigotry?
If Barack Obama wants to be the president of all Americans, he needs to learn how to see things from the perspective of Americans who have beliefs which are very different from his own. He can't simply reflect the most common prejudices or reinforce the lowest common denominator among American Christians. It's not easy to even recognize one's own nonconscious ideologies, much less get past them, but when it comes to a politician who keeps touting himself as an agent of change I don't think that it's too much to ask him to try. I think it's especially important that he find some way to get past any anti-atheist prejudices he may harbor.