Experience has shown that kids who do not participate are often victims of ostracism, threats and other exclusionary practices. Many religious groups are skeptical about organized school prayer because they fear that doctrines and prayers of other religions may be used. Catholics and Protestants have argued for decades over the issue of whose bible should be used. That idea ignores the fact that any and all prayer in public schools is unconstitutional, whether one form of religious ritual is used, or a virtual belief-smorgasbord is presented. That is not the purpose of proposed legislation such as the Religious Equality Amendment.
Students can pray, even in schools if they choose to do so.
They can pray during lunch-breaks, walking or being transported to and from the school, and of course, during their free time. That is clearly wrong, a violation of the separation of government and religion. But I've heard about student-initiated prayer, where the students want to pray. Student populations often reflect the diversity of the culture. Lately, there have been court cases involving this very question.