Well, Chloe, the easy answer is that is violates the Constitutional 1st Amendment that guarantees separation of church and state.
If we have prayer in schoool, a government institution (a publicly funded school) is advancing the cause of religion, and usually a specific religion (in the States, that's usually a Christian one). That subjects non-Christian people unfairly to that religion.
BTW, no problem. Makes me feel like I am studying when I'm sitting here checking posts!