Answer: The courts thought the games were too closely related to school activity.
Santa Fe Independent School District v. Doe is a case in which the U. S. Supreme Court ruled that a policy that allowed student prayer before varsity high-school football games was a violation of the First Amendment's establishment clause, which prohibits the government from establishing, advancing, or giving favour to any religion.
Moreover, the court argued that the school board's policy violated the "Lemon test" which ruled that a statute that does not have a secular, legislative purpose is considered invalid.
The reason why they thought the prayers and the games were "too entangled" was because games could be considered part of school activities. Many students needed to attend these games for athletics or for extra credits, and prayer therefore could be seen as being part of school policy.