<<The Government is far past its rights to do so , there has never been a referendum about this , but I don't think that a safe majority would agree that Prayer is less important .>>
Nobody holds referendums about Constitutional rights. They're there to protect the minority against the majority. At the same time, as a matter of practical politics, no democratically elected government is going to do anything that will genuinely outrage a substantial minority, let alone a majority, of its citizens. If public opinion in favour of school prayer had remained consistently strong since the 1920s, school prayer would never have been abandoned in the public schools.
Prayer in the schools was a given (despite the objections of minorities, specifically Jews, and in total disregard of the constitutional rights of all who objected to religion being "established" in public schools) throughout the entire life of the nation, but during the Cold War, and particularly after Sputnik, I think public opinion began to solidify behind the idea that the Russians were outstripping us in science. Scientific education became a priority here when the idea sank in that mass production of scientists was as important as nurturing the rare scientific genius which both societies had always been able to produce.
Once it became a matter of national security to make science a priority in public education, other concerns which had at one time or another been priorities necessarily shrank in value, religion among them. Advocates of prayer in the public schools, who previously had been seen on one light, now began to be seen as the kind of old-fashioned thinkers, obviously at odds with science, who were responsible for the advantages - - or perhaps perceived advantages - - which the Russian school system had over ours. There was some debate over the true function of the school system, public and private, and seen through Cold War lenses, that function was now one in which science (and non-religious knowledge in general, languages, math, geography, etc.) took on a much more prominent role.
I personally see the school system in general as one for the advancement of knowledge, and religious knowledge and/or instruction in morals and ethics is a part of the knowledge which has to be passed on in the educational process. The only problem is how and where to pass it on. I don't think, in most cases, that leaving it to the parents is the answer. But when one looks at the public educational system, one runs into problems of Constitutional minority rights that do not factor into the non-public components of the educational system. Forcing science students in a publicly run and publicly financed school to sit through, listen to and debate non-scientific alternative explanations of natural phenomena for the sole purpose of exposing them to the views of one or two particular religions, fundamentalist Christianity and Orthodox Judaism, is an unjustifiable waste of the students' time and a blatant breach of the anti-establishment clause of the Constitution. These are views, incredibly stupid and misinformed ones, IMHO, which are available to anyone who is interested in Church, in Church-run schools, Christian Academies, fundamentalist Universities or similar "educational" institutions, but which otherwise have no place in a non-religious institution of learning.