Why is the school prayer issue SO misunderstood?

Look, people can pray ALL they want to in school BECAUSE of the religious freedom guaranteed by the principle of separation of church and state which disallows any REPRESENTATIVE of the school or state (acting in that capacity) to overtly or subtly endorse a particular practice. Why do I get all these persecution emails that say we can't pray in school, then? And why are these facts met with opposition -- they're simple facts! And it happens on both side -- when the principle of separation of church and state was misunderstood and caused a high school to prevent christian students from spreading a religious message (Machusetts, 2003), the ACLU rightfully jumped in and defended the students' rights. Where does the problem lie in not understanding the fact that the law ensures religious freedom by disallowing endorsement by a representative?