There are different ways that faith can be handled in public. One option that many legal systems (from 18th century Europe, through the USSR to ISIS) have used is to have the governmental or quasi-governmental agencies tell you what your faith must be. Another way of doing things, is allowing whatever faith you may have, but limiting the ways that you can express that faith in public. France not allowing Muslim women to wear their hijab to school, or Chinese taking the large crosses down from their churches, or making house churches illegal are examples of this. In America, we've made another choice: pluralism. The first amendment says "Congress can make no law regarding the establishment of a religion or prohibiting the free exercise thereof." What that means (barring some extreme examples) is that I can't make you follow my religion, but you can't stop me from publicly practicing it.
Pluralism isn't perfect. It allows people to have religions really far outside the norms. There are churches of Satanism and of Flying Spaghetti Monsters (a religion that mocks religion). There are religions that emphasize biofeedback and that emphasize sitting in silence to stop all feedback. There are religions that require their adherents to give them a percentage of their money. There are religions that require all members to be celibate. If any of these religions sound awful to you, don't join them. Pluralism allows that too.
Pluralism also isn't total freedom of religion. If a Rastafarian smokes marijuana (which is an important part of Rastafarian-ism), then he doesn't get arrested for being Rastafarian, he gets arrested for smoking pot. If a Muslim wants to sacrifice a goat for Eid-al-Adha, which the Muslim would have to do, they have to be in a place that is zoned for killing animals. If they are not, it is not the religion that gets them arrested, it is the violation of zoning restrictions.
I recently heard about a student who is in trouble here at the University where I teach for openly asking God to help her with her work. Now, I don't know the details. Maybe she was being disruptive when she did this (I know the student, and that would be acting against type, but we all act against type sometimes). Maybe her prayer was interfering with other students getting work done. I don't really know. I sort of think that probably she is in trouble because people don't really understand the First Amendment. They somehow think that a "separation of Church and State" implied by the First Amendment means that a person cannot practice their religion in a "state" area. Or they think that religion needs to be silent on government issues.
And it's not just "fine with me." It has to be fine. Students have the right to the free exercise of their religion. If it's a disruption, then yes, they can suffer the consequences for disruption. If it interferes with the curriculum, then they can get in trouble for interfering with the curriculum. If it is a simple prayer, we cannot prohibit the free exercise of religion. If it is