seperation of church and state?

I read Boulder students protest pledge, under God.
Well while I was reading this article i actually again got a little mad. Even if you don't believe in got or don't belong to the church that really is no reason to not stand or do the pledge. Even people from other countries stand for our pledge when we do it. I have no problem for atheists or people that don't belong to religion but are open to it, I just feel that two words shouldn't keep you from doing something that has been done since the beginning of our country. At the beginning when the U.S. was created they gave you the right of religion and the idea of god in our pledge or on our bills wasn't meant to be apposing it was there just to say that our country was made for good, justice and mabey that we were just plain lucky. In any case I do not believe that two words should keep people from the pledge but since it is free will I guess they have their own judgment over the matter.