Separation of Church and State
What does it really say and mean?
Jefferson had committed himself as President to pursuing the purpose of the First Amendment: preventing the “establishment of a particular form of Christianity” by the Episcopalians, Congregationalists, or any other denomination. Since this was Jefferson’s view concerning religious expression, in his short and polite reply to the Danbury Baptists on January 1, 1802, he assured them that they need not fear; that the free exercise of religion would never be interfered with by the federal government. As he explained:
Gentlemen, – 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... Believing with you that religion is a matter which lies solely between man and his God; that he owes account to none other for his faith or his worship; that the legislative 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. 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 and esteem. 
Jefferson’s reference to “natural rights” invoked an important legal phrase which was part of the rhetoric of that day and which reaffirmed his belief that religious liberties were inalienable rights. While the phrase “natural rights” communicated much to people then, to most citizens today those words mean little.
By definition, “natural rights” included “that which the Books of the Law and the Gospel do contain.”  That is, “natural rights” incorporated what God Himself had guaranteed to man in the Scriptures. Thus, when Jefferson assured the Baptists that by following their “natural rights” they would violate no social duty, he was affirming to them that the free exercise of religion was their inalienable God-given right and therefore was protected from federal regulation or interference.
So clearly did Jefferson understand the Source of America’s inalienable rights that he even doubted whether America could survive if we ever lost that knowledge. He queried:
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 not to be violated but with His wrath? 
Jefferson believed that God, not government, was the Author and Source of our rights and that the government, therefore, was to be prevented from interference with those rights. Very simply, the “fence” of the Webster letter and the “wall” of the Danbury letter were not to limit religious activities in public; rather they were to limit the power of the government to prohibit or interfere with those expressions.