The letter was the subject of intense scrutiny by Jefferson, and he consulted a couple of New England politicians to assure that his words would not offend while still conveying his message: it was not the place of the Congress or the Executive to do anything that might be misconstrued as the establishment of religion.
This is part of my Founding Documents series. The highlighted portions are of my doing.
To messers Nehemiah Dodge, Ephraim Robbins, & Stephen S. Nelson, a committee of the Danbury Baptist association in the state of Connecticut.
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.
(signed) Thomas Jefferson
Never once did President Jefferson promote the removal of G-d, the Creator or the Supreme Being from the United States Government. Instead he was promoting the idea that government has no place in what tenets or beliefs each church, each faith can promote.
In other words: The Government cannot tell the Church how to worship, not the other way around. Something the Supreme Court, ACLU, and the left should remember.