Actually I just disproved your point, you are just too ignorant to understand that. Freedom of speech doesn't allow you to yell obscenities in public, or fire in a theater, etc. And, Freedom of Religion doesn't allow you to proselytize to captive students as an agent of the government. These are restrictions placed on your freedom because they interfere with the freedoms of others. You can't infringe on one person's constitutional rights to allow those of another.
Voluntary initiation and participation in a non-denominational prayer, is not a violation of any other person's right, no one is being forced to pray, it is not something that is mandatory or required. Since this free exercise of religion is not interfering or infringing on another person's right (as mandatory prayer would do), then it isn't unconstitutional, and IS constitutionally protected under the 1st Amendment. The only argument or basis for denying this right, is the fact it is taking place in a government building. But a building doesn't have constitutional rights!