I had no idea this was going on. A 2001 Supreme Court decision ruled that schools could not exclude religious activity on their property on the basis that it violated free speech. Since then the phenomenon of "church planting" has sprung up, where congregations meet in public schools, apparently when classes are not in session. The churches involved are almost all evangelical Christian. Fortunately, a second-circuit court decision ruled against this, and recently the Supreme Court declined to hear an appeal of that decision, which is in this article considered a "small victory."
Rent-free religion in New York's public schools Religion Dispatches