Both the establishment clause and the free-exercise (or anti-discrimination) clauses of the first amendment have been gradually reinterpreted during this period. In some respects, the changes have resulted from the natural process by which cases come before the Supreme Court and further guidance is provided. But also, the Court has shifted in the last several decades in significant ways. More and more, the courts are protecting the exercise of religion more aggressively under the rubric of the anti-discrimination (free exercise) clause of the first amendment. The Courts are making it clear that schools cannot interfere with the expression of religious ideas simply because they are religious. Concurrently, to some extent, the Courts are less likely to find violations of the establishment clause. What this means is that something that might have been prohibited when you were in school, indeed, may well be permitted, because interpretation of the Constitution has changed.
What I studied in law school in the early 1970's about the first amendment groundrules for religion and government is quite out of date. If you think things are different now, well you are right, because the Supreme Court has fundamentally changed its approach to these issues in ways that are far more favorable to free exercise of religion. For a detailed discussion of the establishment clause and free-exercise clauses, try this link.
Impact of No Child Left Behind. Another major factor that has caused local school districts across the country to change the way they approach religion is the No Child Left Behind Act of 2001, which requires the Secretary of Education to issue guidance on constitutionally protected prayer in public elementary and secondary schools. In addition, the law requires that, as a condition of receiving ESEA funds, the State must certify that it has no policy that prevents, or otherwise denies participation in, constitutionally protected prayer in public schools as set forth in the guidance. The Secretary of Education's Guidance has significantly changed practices in many school districts because it has attempted to clarify the groundrules for implementing the first amendment, and the guidance provides significant protections for free exercise.
You can find the Secretary of Education's Guidance on the Internet here. The guidance echos what I have mentioned above:
Now the guidance is just that, a guidance. The truth of the matter is that the Secretary of Education is not charged by the Constitution to interpret the first amendment. But the guidance is an important source of understanding when we look at what is permissible and not permissible. The guidance tells us:
There is much more in the guidance on the topic of prayer in school. Schools must now accommodate requests for release from instructional time for religious purposes in the same way that they would accommodate other requests:
It has long been established that schools have the discretion to dismiss students to off-premises religious instruction, provided that schools do not encourage or discourage participation in such instruction or penalize students for attending or not attending. Similarly, schools may excuse students from class to remove a significant burden on their religious exercise, where doing so would not impose material burdens on other students. For example, it would be lawful for schools to excuse Muslim students briefly from class to enable them to fulfill their religious obligations to pray during Ramadan.
Now this guidance simply does not answer all questions by any means. Application of the rules require judgments as to what imposes "material burdens on other students." Further, the guidance itself is subject to attack by persons who believe that the guidance is a violation of the first amendment in some way. One of the things that most school districts dread is the possibility that they will become embroiled in legal controversy that ultimately leads to significant expense to the district. The most successful districts address these issues by dialog, consensus building, reason, listening, and common sense.
Where school officials have a practice of excusing students from class on the basis of parents' requests for accommodation of nonreligious needs, religiously motivated requests for excusal may not be accorded less favorable treatment. In addition, in some circumstances, based on federal or state constitutional law or pursuant to state statutes, schools may be required to make accommodations that relieve substantial burdens on students' religious exercise. Schools officials are therefore encouraged to consult with their attorneys regarding such obligations.
Keeping out of Trouble by Avoiding Conflict: Educators are not constitutional lawyers, and as I have said, even constitutional scholars have a great deal of difficulty interpreting the first amendment these days. Because first amendment disputes can embroil educators in the Courts, there is a tendency at times to make decisions that avoid conflict and sometimes, an educator will make a decision that is fundamentally wrong, simply because they misunderstand what the rules are. Nobody wants to get sued. Honest people, trying to do the right thing, simply cannot always be expected to apply these complicated rules to perfection. A student writes an essay about Jesus or Moses, or Mohamed and wants to read it aloud in class. Perhaps the teacher, fearing a violation of the establishment clause prohibits the reading, but alas, has violated the free exercise clause. The graduation committee decides to invite a student to give a speech on how Jesus inspires us at graduation, and inadvertently runs afoul of the establishment clause.