Now, if a young child is listening to his teacher, and peers, pray out of a belief other than the ones his parents teach him, what will he think? He will think he is wrong, and do something that means nothing to him.
There's also this:
I am of the Jewish faith. If schools forced me to pray as a Christian, I would raise holy Hell about it (no pun intended). It is not my belief; why must I repeat it?
Not to mention those who don't celebrate the Judeo-Christian faith: Pagans, Muslims, Atheists, Deists, etc.
It's the fact that prayer would be forced.
"How about the kid in fourth grade who gets his butt kicked on the playground 'cause he sat out the prayer?" --Toby Ziegler (Richard Schiff), "The West Wing"
A very good friend of mine plays soccer, and she is Atheist. Before every game, this team does a collective prayer. She says nothing, simply does it with everyone. She tells me it makes her feel very uncomfortable, and tells me her feelings of alienation. The others don't know she's Atheist, except for one girl. They do this, without regard as to other beliefs.
Besides, don't any of these people see that if you start forcing your particular religion down people's throats you wind up with Bosnia, Kosovo, or the Middle East.
School is about children learning. Learning about everything, including accepting others' beliefs. With forced prayer, that's a bit difficult.