there is state money for religious schools; they don't get as much because the state doesn't own the physical plant like they do in the public schools.
When I was going to high school, we got readings read over the loudspeaker in homeroom from a variety of sources, including buddhist, jewish, and muslim, though christian predominated. Not so much a prayer as just a quick thought provoking quote.
However, school control was a lot more decentralised then, and that had a lot more to do with the principal than it did the ministry of education.