Regarding the choice of some governments to regulate religion and thought, Jefferson stated:
The legitimate powers of government extend to such acts only as are injurious to others. But it does me no injury for my neighbor to say there are twenty gods or no god. It neither picks my pocket nor breaks my leg.
Deriving from this statement, Jefferson believed that the Government's relationship with the Church should be indifferent, religion being neither persecuted nor given any special status.
If anything pass in a religious meeting seditiously and contrary to the public peace, let it be punished in the same manner and no otherwise as it had happened in a fair or market.
During his Presidency Jefferson refused to issue proclamations calling for days of prayer and thanksgiving. In a letter to Samuel Miller dated January 23, 1808, Jefferson stated:
But it is only proposed that I should recommend, not prescribe a day of fasting & prayer.
In a letter written to Mordecai Manuel Noah in 1818, Jefferson wrote that America was unique in that it put all religious sects "on an equal footing". This insured that no single religion had state-sponsored domination over any other. However, the state could only do so much; in the same letter, he said that it is up to individuals to behave with religious tolerance towards their neighbors.
https://en.wikipedia.org/wiki/Religious_views_of_Thomas_Jefferson#Separation_of_church_and_state