Patrick Henry at the time was pushing a bill in Virginia that would impose a tax on the citizens for the purpose of supporting Christian Churches.
Knowing what we know of Jefferson, and separation of church and state, it's not hard to imagine that he might wish for Henry's time to come.
Here's the story:
The Virginia Assessment Controversy: the birth of Religious Liberty (morals, reject) - Religious Education Forum
Separation of church and state? What is that?
To clarify, Henry supported the premise the a state should establish a particular denomination church, which all the citizens would be obliged to support.
Jefferson's view was that each person should have the right to worship as they see fit....or not worship at all.
Separation of church and state was to keep the state out of the business of selecting a church...not to keep religion out of government.
In early 1776, as the colonies began to organize independent government, they began to think of statements of basic liberties, and Madison helped craft the Virginia Declaration of Rights, which became the impetus for shedding the establishment of a faith, and the tradition of persecution.
a. George Mason had proposed that the Declaration provide full toleration for dissenters, but Madison would settle for nothing less than “free exercise of religion” for all.
b. At this time most of VirginiaÂ’s leaders still wanted an Anglican [to be called the Episcopal Church after independence] establishment along with the free exercise of religion. Kidd, "God of Liberty," p.53
c. Jefferson explained that “at the time of the revolution, most had become dissenters from the established church but still had to pay contributions to support the pastors of the minority.” “Thomas Jefferson Autobiography,” Ford (ed.), p. 52.
d. So, when Jefferson wrote to the Danbury Baptists in 1802, it was to reassure them the federal government could not interfere in their religious observations, i.e., there is “a wall of separation between church and state.” He wasn’t speaking of religion contaminating the government, but of the government contaminating religious observance.
Many folks misunderstand the way the phrase was being used.