No, they can't. They can't pray anytime, anywhere while in school because they are barred from doing so by the courts in the name of "separation of church and state".
Scripturally, Christians are called to "pray without ceasing" (1 Th 5:17). Theoretically, and in actual practice, they are being barred from doing so.
Meanwhile, Muslims are not only allowed to pray, they are allowed special private space to do what Christians cannot. Hence, what you call "righteous indignation" -- and rightfully so.