There's little controversy over individual, student-sponsored school prayer. What makes people's blood pressure rise is the debate over faculty-led or otherwise school-endorsed prayer—which implies, in the case of public schools, a government endorsement of religion (and usually an endorsement of Christianity, in particular). This violates the establishment clause of the First Amendment and implies that the government does not give equal status to students who don't share the religious views expressed in the prayer.
"Restrictions on School Prayer Violate Religious Freedom."
Restrictions on faculty-led school prayer certainly restrict the government's religious freedom, in much the same way that federal civil rights laws restrict the "rights" of states, but that's what civil liberties are all about: restricting the government's "freedom" so that individuals can live their own lives in peace.
﻿In their official, paid capacity as representatives of the government, public school officials can't publicly endorse religion. This is because if they were to do so, they would be doing so on behalf of the government. Public school officials do, of course, have a constitutional right to express their religious beliefs on their own time.
"School Prayer Is Essential to Developing Students' Moral Character."
This is puzzling because people don't generally look to the government for moral or religious guidance. And it's especially confusing as many of the same people who passionately argue that we need firearms to protect ourselves from the government are so eager to see that same institution placed in charge of their children's souls. Parents, mentors, and church communities seem like more appropriate sources of religious guidance.
"When We Do Not Allow Faculty-Led School Prayer, God Punishes Us Harshly."
The United States is, without question, the wealthiest and most militarily powerful nation on Earth. That's a mighty strange punishment. Some politicians have suggested that the Newtown massacre came about because God wanted revenge on us for prohibiting faculty-led school prayer. There was a time when Christians might have considered it blasphemous to suggest that God murders children to communicate ambiguous, unrelated points, but evangelical communities appear to have a much lower opinion of God than they once did. In any case, the U.S. government is constitutionally prohibited from adopting this sort of theology — or any other sort of theology, for that matter.
"When We Do Allow School Prayer, God Rewards Us."
Again, the U.S. government isn't permitted to take on theological positions. But if we look at the history of our country leading up to the Engel v. Vitale school prayer ruling in 1962, and then look at the history of our country after the ruling, it's clear that the past fifty years have been good to us. Desegregation, women's liberation, the end of the Cold War, a dramatic increase in life expectancy and measurable quality of life — we would have a hard time saying that the United States has not been richly rewarded in the years following the abolition of faculty-led school prayer.
"Most of the Founding Fathers Would Not Have Objected to Public School Prayer."
What the Founding Fathers objected to, or didn't object to, was their own business. What they actually wrote in the Constitution was that "Congress shall make no law respecting an establishment of religion," and it is the Constitution, not the personal beliefs of the Founding Fathers, upon which our legal system is founded.
"School Prayer Is a Public, Symbolic Act, Not a Religious One."
The one accommodation that the establishment clause implicitly makes to Christianity is that it echoes Jesus' suspicions about ostentatious, self-aggrandizing public displays of religiosity. For the sake of our country, and for the sake of our freedom of conscience, that's one accommodation that we would be well-served to honor.