The status of religion generally and prayer in particular are important for America's Christian Right. Many see public schools as a site of indoctrination: kids are already being indoctrinated into communism, secular humanism, and feminism; they would rather have their beliefs promoted by the state with prayer, Bible reading, official religious events, and more. Prayer, though, is a primary focus for their attention. They believe prayer was somehow banned and needs to be restored; in reality, official state-written prayers were eliminated and students can continue to pray on their own all they want.
An outspoken atheist, Madalyn Murray O’Hair has long been an object of hatred and fear for the Religious Right. It is thus not surprising that they placed the blame on her alone for the elimination of state-sponsored prayers and Bible readings in public schools. O’Hair herself certainly didn’t do anything to disabuse people of that notion, and in fact often encouraged it.
In their defense of state-sponsored Bible readings and state-written prayers, opponents of church/state separation sometimes argue that Supreme Court decisions which struck down those activities struck down old, popular traditions. There is a common assumption that the older some practice is, the more it should be exempt from standard constitutional tests. There also seems to be a belief that these decisions struck a serious blow to popular religious practices.
That's right, students should be allowed to pray in school - and they are! Some people act and argue as though students were not permitted to pray in school, but there is no truth to this. At best, they are confusing the difference between official, state-sponsored, state-mandated prayers led by school officials and personal, private prayers initiated and said by the student. At worst, people are being deliberately deceitful in their claims.
Many opponents to church/state separation try to claim that God was "kicked out of schools" back in the 1960s — that God was somehow a part of the standard school day in the 1950s and earlier, but in the evil 1960s God was removed. Since then, it is further alleged, every social ill has gotten worse and the reason for that can be found precisely at the moment when God was expelled. It seems likely that people sincerely believe all of this, but it's not a belief grounded in reality.
Many opponents of church/state separation allege that any growth in social ills like crime, drug abuse, and teen pregnancy are all due to the removal of government-sponsored prayer and Bible reading from public schools. If only these government-sponsored religious activities had been kept, so the argument goes, society would be better off. Therefore, we should reinstitute these special privileges for Christianity and save society from future grief. No part of this argument is true or valid.