Yes, the United States is a Christian (or Judeo-Christian) one, but it is not a “Christian” nation in the sense that Iran or Pakistan, for example are “Islamic Republics.” We have no national church, such as the Church of England in Great Britain, or the Roman Catholic Church in many Latin American countries. Rather, our heritage is Judeo-Christian, and I see no problem in recognizing that fact.
But Jefferson, himself a man of faith, wisely distrusted religious organizations and their hierarchies. He also distrusted the federal government to the same degree.
His famous quote about the "wall" came in his reply to the Danbury Baptist Association after receiving their message expressing concern that the federal government might seek involvement in their affairs. They were concerned that the establishment clause was part of a legislated amendment and thus possibly considered a right granted by government. They desired assurance that freedom of religion be considered an "unalienable" right endowed by the Creator as mentioned by Jefferson in the Declaration of Independence. He assured them it was protected by government, NOT created by it or subject to regulation by it (at least not at the fed level).
Misguided folks quote the wall line while arguing against such innocuous activities as prayers being invoked at graduation ceremonies. These people forget Jeffersons famous letter was written more than a decade after the First Amendment and it closes with then PRESIDENT Jefferson stating "I reciprocate your kind prayers for the protection and blessings of the common Father and Creator of man, and tender you and your religious association, assurances of my high respect and esteem."
Oooops!!! How did that manage to slip through the imagined wall! On the very day it was supposedly built. By the very man who supposedly built it?
Of course, America had state level intermeddlings with religion during Jefferson's day. And, as president, he correctly had no problem with that despite the fact that, as a citizen/guv of VA, he worked against it locally.
Such principled adherence to the Tenth Amendment is extinct today.
The First Amendment only specifies what the FEDERAL gov't can NOT do.
Jefferson was also a political prophet predicting the condition we find ourselves in today. His (and other Founders) fear of "tyranny" and "despotism" coming from the judicial branch are now reality despite their efforts to make it the weakest branch. The Supreme Court now lords over the legislative and executive branches, the states and individuals in ways never intended by Jefferson who said:
"The germ of dissolution of our federal government is in...the federal judiciary; an irresponsible body...working like gravity by night and by day, gaining a little today and a little tomorrow, and advancing its noiseless step like a thief, over the field of jurisdiction, until all shall be usurped from the States.""
Unfortunately, the courts theft of power was complete by the time Chief Justice Rehnquist, in a disgusted dissenting opinion (Jaffree), reminisced about our first President George:
He recalled how Washington, on the very day the First Amendment passed Congress and at THEIR behest, proclaimed a day of "public thanksgiving and prayer, to be observed by acknowledging with grateful hearts the many and signal favors of Almighty God."
Wrote Rehnquist regarding that event: "History must judge whether it was the Father of our country in 1789, or...the Court...which has strayed from the meaning of the Establishment Clause."
"The God who gave us life gave us liberty at the same time...And can the liberties of a nation be thought secure if we have lost the only firm basis, a conviction in the minds of the people that these liberties are the gift of God? That they are to be violated but with His wrath?"
-Thomas Jefferson