First Amendment rights apply differently in schools

First Amendment rights do not apply in schools for either the student or the faculty. I have found no specifics in writing as to exactly what this means. The closest I have come to finding some defined guidelines can be found on the National School Boards Association website. This leaves it open for every first amendment right to be violated to the maximum.
An Indianapolis school has banned only certain websites pertaining to religion which has created controversy with the students and parents.
The Stevenson High School in Lincolnshire shut down their newspaper displaying a blank front page because students were writing about teen pregnancy, shoplifting and students who drink and do drugs. The Chicago Tribune had something to say about the staffs decision to shut down the paper.
For a school to insert their personal opinions or beliefs on any given subject is unjust for the student. Banning specific websites because it doesn't comply with certain Christian ideologies is prejudice. In banning specific websites or free speech sends a message that is not in accordance with the First Amendment. By banning all religious websites is to say that school is no place for religious opinions or beliefs. (Look it up at home). By allowing all religious websites this says that children are free to learn and compare. School is about teaching children how to make informed decisions. When they are not fully informed, they aren't making an informed decision, but are being led to believe that they are. If we only show them certain perspectives how will they learn to be tolerant and open to others? When we only show them what we think is 'the right way' it teaches them prejudice.
Let's look at the definition of prejudice shall we: an unfavorable opinion or feeling formed beforehand, or without knowledge, thought, or reason.
This sounds a lot like what is happening. The kids don't get all the information, therefore, without knowledge.
The United States of America is the land of freedom, is it not? People come here because they are allowed to be who they are here; supposedly.
I am curious to know what you think.