While there is a call for separation of church and state, many of the founders of this country were fleeing religious persecution. So my answer is two fold. First, I believe that the words "Under God" should remain in the pledge as that is how it was written. It has to do with the beliefs of those who founded the country. But secondarily, I do not believe that religion should play a huge role in politics. We are all free to believe as we want to believe and while religion may form your politics, it does not give you the right to force those beliefs on others.
There is a reason that we have written in our countries by-laws to separate church in state. It imposes on our first amendment rights on freedom of religion. Atheist do not believe in god and should not be required to say it. Requiring students to say under God imposes on their freedom of religion.