Answer:
Some people feel so strongly about their religious beliefs that they believe those beliefs should be imposed on others. Prayer in school is one way to achieve this.
Apart from the above, I have difficulty in identifying an argument for prayer in school, but many arguments against the idea. Children who want to pray, to whatever God they believe in, can do so before or after school, or quietly during recess breaks. If people insist on public prayers, mandatory except perhaps on an explicit opt-out basis, they would seem to be attempting to impose their beliefs on other children.