Concerning religion, the 1st Amendment states the following:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof
The only thing the 1st Amendment says, is that you cannot go as far as create a law, telling people how to worship. That is it. References to the separation of church and state principle by our founding fathers, were to describe the above limitation of government, and its influence on religion: it was not to expand the purview of the 1st Amendment, to go beyond what was stated in the 1st Amendment itself. In fact, the following quotation from Thomas Jefferson, said to be the basis of the current interpretation of the 1st Amendment by the Supreme Court, states just that:
"I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church & State."
From a certain perspective, limiting government from going as far creating laws concerning religion, is a separation of church and state. This limitation, separates the government from forcibly regulating how people should worship. Volumes of sayings by our founding fathers indicate they believed the Christian religion, is integral to the integrity of the state. The founding fathers simply did not believe Christianity should be abused by the state, by forcing people to adhere to it with the force of law.
The following quotations, show that the founding fathers did not believe in the current notion of separation of church and state, given by the Supreme Court. The founding fathers actually believed that the Christian religion was essential to the integrity of the state. (They simply believed it should not be abused, by compelling people with the force of law, to adhere to a particular interpretation of it.) (More quotes by our founding fathers, concerning the subject, can be found here.)
Ratifier of the U.S. Constitution
"It cannot be emphasized too strongly or too often that this great nation was founded, not by religionists, but by Christians; not on religions, but on the gospel of Jesus Christ. For this very reason peoples of other faiths have been afforded asylum, prosperity, and freedom of worship here."
--The Trumpet Voice of Freedom: Patrick Henry of Virginia, p. iii.
3rd U.S. President, Drafter and Signer of the Declaration of Independence
"God who gave us life gave us liberty. And can the liberties of a nation be thought secure when we have removed their only firm basis, a conviction in the minds of the people that these liberties are of the Gift of God?
That they are not to be violated but with His wrath? Indeed, I tremble for my country when I reflect that God is just; that His justice cannot sleep forever..."
--Notes on the State of Virginia, Query XVIII, p. 237.
"I am a real Christian – that is to say, a disciple of the doctrines of Jesus Christ."
--The Writings of Thomas Jefferson, p. 385.
2nd U.S. President and Signer of the Declaration of Independence
"Suppose a nation in some distant Region should take the Bible for their only law Book, and every member should regulate his conduct by the precepts there exhibited! Every member would be obliged in conscience, to temperance, frugality, and industry; to justice, kindness, and charity towards his fellow men; and to piety, love, and reverence toward Almighty God ... What a Eutopia, what a Paradise would this region be."
--Diary and Autobiography of John Adams, Vol. III, p. 9.
"The general principles, on which the Fathers achieved independence, were the only Principles in which that beautiful Assembly of young Gentlemen could Unite, and these Principles only could be intended by them in their address, or by me in my answer. And what were these general Principles? I answer, the general Principles of Christianity, in which all these Sects were United: And the general Principles of English and American Liberty...
"Now I will avow, that I then believe, and now believe, that those general Principles of Christianity, are as eternal and immutable, as the Existence and Attributes of God; and that those Principles of Liberty, are as unalterable as human Nature and our terrestrial, mundane System."
--Adams wrote this on June 28, 1813, excerpt from a letter to Thomas Jefferson.
"The second day of July, 1776, will be the most memorable epoch in the history of America. I am apt to believe that it will be celebrated by succeeding generations as the great anniversary Festival. It ought to be commemorated, as the Day of Deliverance, by solemn acts of devotion to God Almighty. It ought to be solemnized with pomp and parade, with shows, games, sports, guns, bells, bonfires and illuminations, from one end of this continent to the other, from this time forward forever."
--Adams wrote this in a letter to his wife, Abigail, on July 3, 1776.
The Supreme Court therefore, in my opinion, erred in its use of the separation of church and state principle, espoused by Thomas Jefferson. Jefferson pointed to the principle on display in the 1st Amendment, which limited government from passing laws, concerning how people should worship - in his letter to the Danbury Baptist Association in Connecticut, in 1802. Jefferson was not seeking to expand the bounds of the 1st Amendment in a mere personal letter, or espouse the idea that Christianity / religion should be strictly or near strictly excised from the state - which other writings by him and other founding fathers, soundly contradict.