The short answer to the question, "what's wrong with prayer in schools?", public private or otherwise, is "not a thing." To quote an overused phrase, "as long as their are tests, there will always be prayer in schools." The first ammendment to the Constitution guarrantees the free exercise of religion and there is no law that can be permitted to infringe upon that right and contrary to much of the rhetoric out there, the Supreme Court's 1962 decision on school prayer did nothing to change that law. Your children and mine are free to pray as their consciences and their religious traditions require them too.
What the decision did do, along with the accompanying decision on reading the Bible in the public schools, was to render public school SPONSORED prayer illegal as a violation of the first ammendment. Rather than eliminate your child's right to pray in school, the court protected that right by making it illegal for any public school or other government agency to dictate to your child how, when and to whom they should pray. Up until that decision became law, schools all across this nation were allowed, (and many did)require students to read the Protestant Bible and to recite Protestant Christian prayers at designated times during the school day effectively staking out the public schools of America as Protestant schools. This was a large part of the reason that Roman Catholics set up a parallel set of schools all over the country- so that their children could go to school without having to pray prayers and read bibles that were not sanctioned by their faith. If you were Catholic, or Jewish, or any other religion or no religion, the message was clear: this is a Protestant Christian nation, our institutions, our culture, they are Protestant Christian. Cultural domination is as much what this issue is about as any concerns for piety.
I think the same can be said about posting the Ten Commandments in court houses and schools. Arguments are made that the Ten Commandments are a good ethical code that is beneficial to all as well as a part of the heritage of Christians and Jews (Muslims too by the way). And yet, one wonders what the advocates for displays of the Ten Commandments would say to posting the Muslim version instead of the one used by most Protestants- or even the Roman Catholic version. In this case, as in the case of most of these issues from the War on Christmas to school-sponsored prayer the issue seems ultimately to come down to who owns the culture- about whether this nation belongs to all of us, or just some of us.
As a religious person, I appeal to other religious persons to think carefully as to whether we really want to trust the public schools for our children's prayer lives or religious educations. I know that for me, I reserve the right to teach my children about prayer, about the Ten Commandments, about the tenets of my faith at my home and in my church. I don't want a public school telling my kids who to pray to or how to pray. I don't need the Ten Commandments to stare at me or mine from the courthouse either, they are written on my heart and posted in my church, where they belong. Posting them is not the issue- living them is.
As an American, I recognize the right of every American to follow the dictates of his or her own conscience as I follow the dictates of mine. I recognize their right to to be full stakeholders in this democracy just as I am, equal before the law, whether they worship as I do or not at all. How about you? If you do, I urge you to join us at the Interfaith Alliance. Because you only have the rights you are willing to defend.