For many, I'll assume they think it means keeping church or religion out of all government and government supported entities. Wrong.
I'm sure many would prefer that scenario, however, to understand this phrase we need to examine two items: the First Amendment and Thomas Jefferson's letter to the Danbury Baptists.
The First Amendment to the U.S. Constitution:
"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances."
Let's break it down:
1) Congress cannot make a law or laws that establishes a national religion or the preference of one religion over another, non-religion over religion, or religion over non-religion.
2) Congress cannot make a law or laws that prohibits people from worshiping how they wish.
3) Congress cannot make a law or laws that prohibits people, groups of people, or the press from speaking and communicating their thoughts or information.
4) Congress cannot make a law or laws that prohibits people from peacefully gathering (be careful activists...your freedom to speak can be overshadowed if your assembly is not peaceful).
5) Congress cannot make a law or laws that prohibits people the freedom to petition the government to correct an injustice. They can do so without fear of punishment.
The second part of understanding "separation of church and state" is the Danbury Baptist letter.
Jefferson wrote a letter to the Danbury Baptist Association in 1802 to answer a letter from them written in October 1801. The Danbury Baptists were a religious minority in Connecticut, and they complained that in their state, the religious liberties they enjoyed were not seen as immutable rights, but as privileges granted by the legislature - as "favors granted." Jefferson's reply did not address their concerns about problems with state establishment of religion - only of establishment on the national level.
Here's the letter written to Thomas Jefferson:
The address of the Danbury Baptists Association in the state of Connecticut, assembled October 7, 1801.
To Thomas Jefferson, Esq., President of the United States of America.
Among the many million in America and Europe who rejoice in your election to office; we embrace the first opportunity which we have enjoyed in our collective capacity, since your inauguration, to express our great satisfaction, in your appointment to the chief magistracy in the United States: And though our mode of expression may be less courtly and pompous than what many others clothe their addresses with, we beg you, sir, to believe that none are more sincere. Our sentiments are uniformly on the side of religious liberty--that religion is at all times and places a matter between God and individuals--that no man ought to suffer in name, person, or effects on account of his religious opinions--that the legitimate power of civil government extends no further than to punish the man who works ill to his neighbors; But, sir, our constitution of government is not specific. Our ancient charter together with the law made coincident therewith, were adopted as the basis of our government, at the time of our revolution; and such had been our laws and usages, and such still are; that religion is considered as the first object of legislation; and therefore what religious privileges we enjoy (as a minor part of the state) we enjoy as favors granted, and not as inalienable rights; and these favors we receive at the expense of such degrading acknowledgments as are inconsistent with the rights of freemen. It is not to be wondered at therefore; if those who seek after power and gain under the pretense of government and religion should reproach their fellow men--should reproach their order magistrate, as a enemy of religion, law, and good order, because he will not, dare not, assume the prerogatives of Jehovah and make laws to govern the kingdom of Christ. Sir, we are sensible that the president of the United States is not the national legislator, and also sensible that the national government cannot destroy the laws of each state; but our hopes are strong that the sentiments of our beloved president, which have had such genial effect already, like the radiant beams of the sun, will shine and prevail through all these states and all the world, till hierarchy and tyranny be destroyed from the earth. Sir, when we reflect on your past services, and see a glow of philanthropy and good will shining forth in a course of more than thirty years we have reason to believe that America's God has raised you up to fill the chair of state out of that goodwill which he bears to the millions which you preside over. May God strengthen you for your arduous task which providence and the voice of the people have called you to sustain and support you enjoy administration against all the predetermined opposition of those who wish to raise to wealth and importance on the poverty and subjection of the people. And may the Lord preserve you safe from every evil and bring you at last to his heavenly kingdom through Jesus Christ our Glorious Mediator.
Signed in behalf of the association,
Stephen S. Nelson
And Thomas Jefferson's response (Note: The bracketed section in the second paragraph was blocked off for deletion in the final draft of the letter sent to the Danbury Baptists, though it was not actually deleted in his draft of the letter. It is included here for completeness. Reflecting upon his knowledge that the letter was far from a mere personal correspondence, Jefferson deleted the block, he noted in the margin, to avoid offending members of his party in the eastern states.):
To messers Nehemiah Dodge, Ephraim Robbins, & Stephen S. Nelson
a committee of the Danbury Baptist association in the state of Connecticut.
The affectionate sentiments of esteem & approbation which you are so good as to express towards me, on behalf of the Danbury Baptist association, give me the highest satisfaction. My duties dictate a faithful & zealous pursuit of the interests of my constituents, and in proportion as they are persuaded of my fidelity to those duties, the discharge of them becomes more & more pleasing. Believing with you that religion is a matter which lies solely between man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, and not opinions, 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 and state. [Congress thus inhibited from acts respecting religion, and the Executive authorized only to execute their acts, I have refrained from presenting even occasional performances of devotion presented indeed legally where an Executive is the legal head of a national church, but subject here, as religious exercises only to the voluntary regulations and discipline of each respective sect.] Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties. I reciprocate your kind prayers for the protection and blessing of the common Father and creator of man, and tender you for yourselves and your religious association, assurances of my high respect & esteem.
(signed) Thomas Jefferson Jan.1.1802.
When the First Amendment was passed it only had two purposes:
1) There would be no established, national church for the united thirteen states. To say it another way: there would be no "Church of the United States." The government is prohibited from setting up a state religion, such as Britain has, but no barriers will be erected against the practice of any religion. Never was the intention for our governing bodies to be "separated" from Christianity and its principles. The "wall" was to protect the church from the state. The world was not to corrupt the church, yet the church was free to teach the people Biblical values. It keeps the government from running the church but makes sure that Christian principles will always stay in government.
2) The second purpose of the First Amendment was the very opposite from what is being made of it today. It states expressly that government should not impede or interfere with the free practice of religion. The purpose of the separation of church and state in American society is not to exclude the voice of religion from public debate, but to provide a context of religious freedom where the insights of each religious tradition can be set forth and tested.
The First Amendment, which prohibited any "law respecting the establishment of religion or prohibiting the free exercise thereof," has evolved into something entirely new. During the last generation, the courts, at all levels, have ruled in ways that essentially guarantee the freedom from religion, instead of the freedom of religion.
"Separation of church and state," as applied to education, means that a prayer at a graduation ceremony is unconstitutional. It also means that students may not pause for a moment of silence at the beginning of their school day. It means that a nativity scene may not be displayed on public property unless there are other displays (e.g. Santa Clause or Christmas trees) that secularize the presentation.
Today's conception of "separation of church and state" has also been used to remove historic crosses from public property, and religious symbols from city seals. It has been used to remove the Ten Commandments from courtrooms, even though they are carved in stone within the architecture of the Supreme Court building. The concept has been used to prevent religious expressions on personalized license plates. And these are but a few of the official applications of the concept, or “law” of "separation of church and state."
One should understand that "separation of church and state" is not actually a law. It is a doctrine, or a legal concept, that has been implemented by the various courts primarily over the last fifty years. If this concept, as originally understood, would have been applied with consistency over the years, America would certainly be a different country right now. Religious expression would flourish, and the courts would not be micromanaging the religious life of the American people.
The doctrine of "separation of church and state" has been used, and is being used, to effectively purge religion from the public square. The historical perspective on church/state issues reveals a much different story. The government was to accommodate the religious communities; religion and religious expression were to be encouraged.