Here's a copy paste from another comment I made on this thread.

You need to be familiar with the first amendment. Two parts, Establishment Clause and Free Exercise Clause. One says government won't make laws regarding religion; AKA no state sponsored religions. This sometimes conflicts with the Free Exercise clause which says government won't prohibit the exercise of one's religious rights. In this case, the government isn't sponsoring one religion over another, they are simply allowing religion to exist. One could argue, as you are, that the government is showing preferential treatment towards religion over non-religion. According to the Supreme Court (Abington Township v. Schempp 1963) the law (or in this case, action of the government) must have a secular purpose, and its primary effect must not be to promote or inhibit a particular religion. Are Air Force invocations for a secular purpose? No. It fails the test, therefore is unconstitutional via the Supreme Court's reasoning. Another case, which seems to conflict with the logic of "shut up and stand in silence while people pray," is (Wallace v. Jaffree 1985) The summary of the case is, Alabama passed a law for a daily moment of silence in school for private prayer, it was struck down, because it did not pass the secular purpose test. This is comparing apples and oranges some might say. A law specifically for prayer, this is an event where people can choose not to participate. Just be respectful! According to the Supreme Court, you're wrong (Lee v. Weisman 1992). The summary of this case, was there was a non-sectarian prayer at a voluntary event, where participation in the prayer of the event was also voluntary. Double voluntary? That means no coercion right? Wrong. Just like some Air Force events are "voluntary" it is still expected you attend. Also, even though the act of praying is voluntary, it still imposes indirect public and peer pressure on attendees of events. In all of these examples it has been removing the influence of religion from the live's of children. In school teacher's have ultimate authority and influence your success. You seek to be accepted by your classmates. Does the same not apply to the Air Force? Commanders with power, wanting to be accepted in work stations, flight etc. When you're already free to practice religion without burdening others, why MUST you burden others? TL:DR Secularization takes time.