Tax support of churches in America was nothing new, or anything particularly unique to Virginia. Massachusetts supported its congregationalist system in a similar manner. The reasons for this were steeped in a belief that religion and moral guidance would be needed to maintain a society. However, this lack of religious tolerance came to the forefront in the 1770's, as Virginia became deeply involved American War for Independence. What followed, as John Ragosta states in his work on Virginia dissenters, "What followed was not principled liberalization, but a complex negotiation for mobilization with piecemeal reforms paralleling military necessity as Virginia's political leaders sought to obtain the support of dissenters without wholly abandoning their established church. Anglicans objected vociferously, insisting that the contingent support offered by dissenters was unpatriotic. By the end of the war, the establishment had been forced to eliminate church taxes and penalties for nonattendance, to liberalize provisions on marriage, and to limit the civil functions of Anglican vestries."
In the immediate postwar era, various groups and individuals sought to re-implement some sort a church subsidy, led by prominent patriots like Patrick Henry. Unlike prior assessment configurations, however, the taxes could support the church of the individuals choice. This proposed bill was ultimately opposed and failed to become law due to the efforts of James Madison. Furthermore, dissenters worked to overturn previous laws that had been perceived to grant special privileges to the Episcopal church. Presbyterians and Baptists who had been on the receiving end of outright persecution were reluctant to give the Anglicans any room to reclaim their old official position. Subsequent endeavors as late as the 1840's to resurrect the earlier assessment laws also met heavy debate and opposition.
Thomas Jefferson assured a group of wary Baptists in 1802 that there was nothing that the Federal Government could legally do to interfere with the religious affairs of American citizens, citing a “wall of separation between church and state.” Religious dissenters had helped win their own freedom and security in Virginia during the period of the American Revolution, after which they sought to protect that hard fought recognition. It was through this struggle that the American ideal of religious toleration was finally realized in the early republic.
Benner, Dave: "Jefferson's True Wall of Separation" The Abbeville Blog, August 12th, 2016.
Buckley, Thomas E.: “After Disestablishment: Thomas Jefferson's Wall of Separation in Antebellum Virginia,” Journal of Southern History (1995): 445-480. http://www.jstor.org/stable/pdf/2211869.pdf?_=1469564858217
Dreisbach, Daniel: “A New Perspective on Jefferson’s Views on Church and State Relations: The Virginia Statute for Religious Freedom in its Legislative Context” The American Journal of Legal History (April 1991)
Hutson, James: “Religion and the State Governments,” in “Religion and the American Founding,” the Library of Congress: http://www.loc.gov/exhibits/religion/rel05.html
Ragosta, John A.: “Virginians Dissent,” in Wellspring of Liberty: How Virginia's Religious Dissenters Helped Win the American Revolution and Secured Religious Liberty (Oxford, 2010)