Are only certain people entitled to "religious freedom"?

I am atheist, so frankly I have no stake in the argument. Having said that, I have noticed the following: Islamists who want to build an Islamic center near ground zero are entitled to do so because America is founded on the principle of religious freedom. Christians who want to say a prayer in school are not entitled to do so because, well, because they have no such religious freedom. So why do some folks get the “religious freedom” pass, and others do not?