Of course the fact that students may pray in school of their own accord, provided it's not at the behest of the state, or that such prayer does not interfere with official school functions, or is otherwise not disruptive, isn't the issue for conservatives. For Christian fundamentalists and the social right the issue isn't one of a right to religious expression, it's their frustration with being denied a political weapon that is religion in general, and Christianity in particular.
By compelling Christian prayer in public schools, conservatives seek to send a clear message to non-Christians that they are not part of the political community, that non-Christians are unwanted and unwelcome, and that those of a minority faith, or altogether free from faith, are to be relegated to an outsider status, a consequence of their being subject to 'Christian majority rule.'
It's further confirmation of the arrogance of most Christians, and the fundamental authoritarian nature of conservatives.