Of course, "separation of church and state" was a phrase used by Thomas Jefferson in a letter to The Danbury Baptists in 1802. This is the version of the letter that Jefferson sent:
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 and 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 and zealous pursuit of the interests of my constituents, & in proportion as they are persuaded of my fidelity to those duties, the discharge of them becomes more and 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, & 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 & State. 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 & blessing of the common father and creator of man, and tender you for yourselves & your religious association, assurances of my high respect & esteem.
Jan. 1. 1802 [emphasis mine]
Jefferson, who wrote in 1776 that "all men were created equal" and that our rights were "Endowed by our Creator", was not a member of the Constitutional convention and played no part in the writing or ratification of the Constitution.
Note though that Jefferson, in his Danbury letter (which is a personal letter and has no force of law, let alone Constitutional law) did use language similar to that of the Constitution itself. He referred to a wall of separation between church and state. This echos the actual Constitution, which states "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof. "
What is prohibited by the Constitution is an institutional relationship between church and state. That's what "establishment" means. The Constitution requires that there be no national church. It does not in any way proscribe public religious expression by private citizens or by government officials.
Presidents, including Jefferson, routinely refer to God in public statements. Lincoln, perhaps the least formally religious of of the pre-Obama presidents, delivered a Second Inaugural Address that was essentially a sermon. These are the religious statements in Lincoln's speech (thank goodness that Lincoln wasn't giving a high school graduation speech!):
...Both read the same Bible, and pray to the same God; and each invokes his aid against the other. It may seem strange that any men should dare to ask a just God's assistance in wringing their bread from the sweat of other men's faces; but let us judge not, that we be not judged. The prayers of both could not be answered—that of neither has been answered fully.
The Almighty has his own purposes. "Woe unto the world because of offenses! for it must needs be that offenses come; but woe to that man by whom the offense cometh." If we shall suppose that American slavery is one of those offenses which, in the providence of God, must needs come, but which, having continued through his appointed time, he now wills to remove, and that he gives to both North and South this terrible war, as the woe due to those by whom the offense came, shall we discern therein any departure from those divine attributes which the believers in a living God always ascribe to him? Fondly do we hope—fervently do we pray—that this mighty scourge of war may speedily pass away. Yet, if God wills that it continue until all the wealth piled by the bondman's two hundred and fifty years of unrequited toil shall be sunk, and until every drop of blood drawn with the lash shall be paid by another drawn with the sword, as was said three thousand years ago, so still it must be said, "The judgments of the Lord are true and righteous altogether."...
Public statements by government officials at all levels have always been replete with assertions of religious belief. Their Constitutionality is unchallenged, because what is prohibited by the First Amendment is the institutional establishment of a national church, not religious speech.
There is no constraint in the Constitution or in the concept of 'wall of separation between church and state' of the use of religious words or themes in public by public officials.
Well, the words "separation of church and state" are not in the US Constitution, but neither are the words "right to a fair trial". Yet I doubt Egnor would make the same claim about the right to a fair trial.
Actually, the right to fair trial is very clearly guaranteed in the Fifth Amendment:
No person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a Grand Jury, except in cases arising in the land or naval forces, or in the Militia, when in actual service in time of War or public danger; nor shall any person be subject for the same offense to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation.The Fourteenth Amendment guarantees "equal protection of the law". The right to a fair trial is quite clearly stated in the Constitution.
Contra Shallit, the atheist doctrine of expungement of religious speech from the public square is nowhere to be found in the Constitution or in any coherent Constitutional doctrine.
'Separation of church and state', understood as prohibition of an established institutional church, is a reasonable interpretation of Constitutional doctrine. But the Constitution does not prohibit in any way the use of religious language by public officials. Such religious speech has been used by public officials at all levels of government since our founding (we have a National Day of Prayer, In God We Trust on our currency, and 'under God" is in our Pledge of Allegiance, for goodness sake).
The drive to extinguish all references to God in public/government forums is merely atheist suppression of the rights of all Americans to freedom of speech and freedom of religion.
Atheists are instinctive totalitarians. When they have state power, they are always totalitarians. When they lack state power, they do all they can to impose their personal irreligious beliefs on others by co-opting legal force.
No one forces atheists to pray or to participate in any religious act. It is atheists who use force to silence those who express different beliefs.