As with a lot of controversial issues, this problem has its root in fundamentalism, and the dangers thereof.

Historical situation: Fundamentalist Christians established the American school system back in colonial days (America was founded by puritans). Prayer was mandatory, and nobody complained, since practically everyone back then was Christian. And those that weren't quickly became human firewood.

Progression: More and more people have come to disown the Christian faith - either as rebellion against their peers/parents, or because it doesn't fit in with their world view.

Current situation: There are now, arguably, more people in American schools who couldn't give a fuck about God, than people that do. These people do not want to pray to God, and certainly do not wish to be forced to.

Reaction by fundamentalist groups: Apply pressure to school boards and legislators to enforce school prayer - and thus a belief system - onto students by having them pray at school.

Problem: Freedom of religion prevents schools from favoring one religious belief system over the other.

Problem with aforementioned problem: Fundamentalist groups are convinced that the other religious belief systems are hoaxes and conjured up by the Devil, and thusly do not give a fuck. There should be no choice in the matter.

Problem with the whole thing: Some people agree with the fundamentalist views.

Possible solution: Free choice. Let the individual choose for him/herself whether they want to participate in organized prayer.

Problem with possible solution: People can't think for themselves.

Situation: Unsolveable.