Bill Poser at Language Log argues that the words 'under God' in the pledge of allegiance are indeed unconstitutional, as the 9th Circuit court ruled in 2002. It's now going before the Supreme Court, so it will be making the rounds once again. His main point is that it "violates the freedom of religion of those who do not believe in God or who do not consider the United States to be a nation under God." Now I don't see any reason why we need to have those words there. Their origin in the pledge is a little suspect. I don't see how it's persecution of Christians to remove them. Removing them doesn't harm Christians' liberty in any way, and not everyone who wants them removed hates Christians. Still, I'm not sure how having some words in a statement violates anyone's freedom.
Even if the government were to pass a law declaring the existence of God, that wouldn't violate anyone's freedom. Such a law wouldn't make it illegal to believe that there's no God, nor would it prevent you from saying that there's no God. The laws states it as a fact but doesn't force you to say it as one. It just states in the law that God does in fact exist and then adds no normative consequences.
I don't see how the pledge of allegiance is any different except for its being less severe than a law stating that there's a God, since our government's actual laws are neutral on that issue. I'm not even sure the pledge of allegiance has any legal significance. I don't think you have to say it to become a citizen (I was at my wife's interview, and I know they didn't make her say it there). You don't have to say it at any point to remain a citizen. I don't think you have to say it to be in the military (just an oath to uphold the Constitution, which doesn't include the pledge). It seems to me to be on the same order as RI having the Rhode Island Red as the state bird and coffee milk as the state bird. What if you don't like coffee milk? I certainly don't. Does that give me a reason to get mad at the government of the state where I was born and lived for 22 years? It's true that public schools do have an event in the morning at which most students recite the pledge, but that's not a government-enforced saying (and it's in fact illegal to enforce it because of freedom of religion).
Poser's main objection to this argument is that some schools do enforce it illegally. So? Some religious groups use coercive behavior to get people into their cult. Does that mean religion should be outlawed? The existence of people breaking the law to get people to say something that they have the legal freedom not to say is not a reason to say that the words in that phrase are violating anyone's freedom of religion. The rogue teachers and administrators who illegally force kids to say the pledge are the ones violating people's religious freedom, not the mere presence of those words in an optionally utterable statement. If the Supreme Court gives in on this one, they're not thinking straight.