Because the majority (that's MAJORITY) of the people in this country are Christian.
However, if the prayer is nondenominational (IE: doesn't mention Jesus, Allah, Baal, or whoever one worships), what's the big deal? If it's a silent prayer, who frakkin' cares?
A majority of the people cannot limit access of a minority of people in this nation. It's antithetical to the Constitution.
If they're giving special favors (such as free advertising) to one group, they must give it to all groups.