Where has our Freedom of Religion Gone?

Looking back, there was a time when prayers were offered in classrooms daily, along with the Pledge of Allegiance.  That is no longer the case.  I came across an article from 1962 in the Othello Outlook.  It talks about secularism vs religion in the school:
7/12/62 Prayer In Our Schools?  Guest Editorial
Editorial Note: Following statement on recent Supreme Court decision on prayer in public school was made my Most Rev. Bernard L. Topel, Phd, Bishop of Catholic Diocese of Spokane (Which includes Adams County).  It appeared in Inland Register, diocesan newspaper, Friday July 6.
Supreme Court and Secularism
“It is time to speak out boldly.  It is time for action.  In fact, it is long past time for both.
I refer to the growing series of decision of the Supreme Court that are stifling religion and (in effect) promoting immorality.  A new low was reached in two recent decisions of the Supreme Court.
The first declared unconstitutional the recitation in public school of the following prayer:
“Almighty God, we acknowledge our dependence upon Thee and we beg Thy blessing upon us, our parents, our teachers, and our country.”
No question this prayer promotes religion, no question too it promotes no particular relation.  The Supreme Court declared the recitation of this prayer unconstitutional on the basis of the First Amendment.  The fact is, though, that those who wrote, proposed and voted for the first Amendment of the Constitution wanted religion promoted, the while they wanted no particular sect favored.
How has this great change come to pass?  How has it come that the Supreme Court makes decisions so contrary to the thinking of one hundred years ago?  One word gives the answer: secularism.
The majority decision contained these words: “It is no part of the business of government to compose official prayers for any group of American people to recite as part of a religious program carried on by the government.”  Millions of Americans, I hope, disagree with this.  Any true believer of God knows that God should be—indeed, must be recognized by the state.  In fact, the state which does not, one day (in God’s good time) will suffer for that sinful neglect.  It cannot be otherwise. 
Many eminent constitutional lawyer also disagree with the decision.  After all, there is nothing infallible about the decision of the majority of the nine men who make up the Supreme Court.  The views of the individual Justices, their attitudes, color their interpretation of the Constitution.  Apparently, the mind of the nine Justices or our Supreme Court have for far too long been colored by secularistic thinking.
A very bad effect on morals has also resulted from another series of Supreme Court decisions, notable those that have to do with obscene literature.  Due to these decisions, it has become almost impossible to stop the flow of vile, salacious and immoral literature.  The most recent decision of the Court, in my opinion, reaches a new low.  This decision ruled that the United States Post Office authorities were wrong in prohibiting the use of the mails to magazines (to use the words of the Supreme Court,) that  “are primarily composed, if not exclusively, for homosexuals, and have no literary, scientific or other merit.”  Moreover there is the admission by the Court that these magazines do promote “prurient interest” in homosexuals.  The result of this decision is complete liberty for magazines to reach these unfortunates no matter how harmful they may be.
So I repeat, the time has come for action.  No longer can we tolerate such abuse of religions and morality.
If the appointment of Supreme Court Judges with less secularistic outlook will bring about the change, then this must be done.
If it means new laws must be passed, then let them be passed.
If it means a new constitutional amendment must be drawn, then in God’s name, let that be done.
It is of more than passing moment that these words will be read by you right after the 4th of July.  Independence Day is a day of great joy because it marks the birth of independence for us Americans.  God forbid that it will ever mean independence from Him and from morality. 
These rulings outlined any prescribed prayer, not prayer itself.  The rulings of the Supreme Court affirmed, that government could not force the exclusion of religion in schools "in the sense of affirmatively opposing or showing hostility to religion."
But bit by bit, the opposite has happened.  Where has our right to pray in school gone?  The constitutions says two things on this subject.  "Amendment I: Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;"  From there, how do we get to where we are today.  Note, there is no separation of church and state.  (That is a Thomas Jefferson quote, and would have been in the Constitution if they intended it to be there.)  It expressly prohibits any law respecting the free exercise of religion.  So we have the right to pray in school, we have the right to say Christmas (not holiday.)  In the changes that have been made secularism and atheism are the only winners, and are not they putting themselves in the place of religion. Are they not now state sponsored religions.  As the Bishop noted,  we must stand up and demand our rights.  We have the right to worship in the military and in public areas.  A cross in a military cemetery is not a government promoting a religion.  Forcing citizens to take it down would be.