The students were considered illegally absent until re-addmitted. The state declared that there was no clear and present danger when the students remained passive during the pledge. Religion is a big concern in Public Schools. There are a lot of different beliefs when it comes to praying in schools. Students deserve to be treated equal in schools and, according to the government, if it means eliminating Religion issues than so be it.
School is a place for students to learn.
Religion can be practiced privately at home or in church. An Overall View of Religious Liberty Defined By US Supreme Court Cases. September 20, 2000.