First, nothing prevents students from praying anytime they want in school. Many do it all the time, especially on exam days. Students can pray individually and they can get together and pray in groups. What is not allowed is for the school to require students to pray. There are many reasons for this prohibition. The primary one is that the US Constitution does not allow it. This has been confirmed in multiple court cases all over the country. A secondary reason is that it creates a hostile environment for students who do not accept that prayer. This is not just an atheist issue. There are many religions in the world besides Christianity and many of them are opposed to prayer in public school. Public schools need to be inclusive, not exclusive. Religious prayer does nothing but cause divisions.
Second, Christian attempts to put prayer into schools run directly counter to biblical teachings. Jesus said prayer should be a private affair devoid of public display: "And when you pray, you must not be like the hypocrites; for they love to stand and pray in the synagogues and at the street corners, that they may be seen by men. Truly, I say to you they have received their reward. But when you pray, go into your room (or closet.) and shut the door and pray to your Father who is in secret..." (Matthew 6:5-6 RSV). Now, I give no consideration that this bible verse has any relevance since I am not a Christian. However, this verse should be relevant to Christians who believe that the bible is god’s law to mankind. What always surprises me is that some Christians want the government to decide on what type of prayer their children should engage in. After all, they might choose the wrong one. :)
The reasons are a lack of parental involvement, a dumbing down of the educational standards and a lack of authority and consequences for poor behaviors when students act up. The schools have been overwhelmed by illegal aliens in many states as well. The US school system is in trouble and needs to be re-tooled. However, we waste valuable time when we debate this non-issue.