Once upon a time all Presbyterians adhered to the Westminster Confession of Faith. But during the American Revolutionary period, in order to seek to justify their political conduct, the American Presbyterian churches revised the Westminster Confession of Faith and Catechism concerning the civil magistrate. The webpage at http://www.upper-register.com/theonomy/1788_revision_parallel.html shows the nature of those amendments, with a parallel comparison of the original versus the American amendment.
For instance, the American amendment removed the clause from the Catechism that said ‘tolerating a false religion’ was a sin. The American amendment revised chapter 20 of the Westminster Confession, which originally had indicated the civil magistrate as well as the church had roles in suppressing religious errors in doctrine and worship. The American amendment effectively rejected such suppression by the magistrate. The American amendment also amended paragraph 3 of chapter 23 significantly. Gone were the statements about the duty of the magistrate to suppress heresy and idolatry, and gone too were the statements which called for church establishment. They were replaced by statements which indicated the civil magistrate should not show preference for one denomination over another, nor hinder free religious exercise. This effectively prohibited suppression of heresy, idolatry, blasphemy, etc., thus legalizing the idolatrous Mass, etc.
Leading the amendment movement was a transplanted Scot named John Witherspoon. John Witherspoon (1723-1794) was the president of Princeton University, a signer of the Declaration of Independence, and a ratifier of the U.S. Constitution. Both the Declaration of Independence and the US Constitution that Witherspoon supported rest upon premises foreign to the historic reformed faith. He served on over 100 committees in Congress and was head of the Board of War (essentially, he was the congressional "boss" for Commander-in-Chief George Washington). Witherspoon promoted the Common Sense philosophy he had adopted from Moderatists and “Enlightenment” philosophers back in Scotland, and this Common Sense philosophy formed the intellectual framework for American Presbyterian-style political philosophy. Common Sense philosophy undermines the reformed doctrine of total depravity, and fails to recognize man’s need for divine special revelation to govern society. Under Witherspoon’s intellectual leadership, American Presbyterians played no small role in effecting the American Revolution.
The amendment movement was in direct contradiction to the Protestant Reformation. It led to the institution of arguably the first secularist nation in world history: the USA. American Presbyterians joined with all sorts of heretics and infidels to engage in their revolution, overthrow established Protestantism, and raise up a nation founded on secularist principles. This secularist nation has been the foundational model for other secularist political schemes which have come to dominate the modern era. Her symbol is Lady Liberty, also called Liberty Enlightening the World, for her secularist model has been imitated the world over. This model was certainly in direct contradiction to the doctrines taught in the original Westminster Standards subscribed to by the Free Presbyterian Church of Scotland. More importantly, it contradicted scriptural principles, such as the duty of the civil magistrate to enforce both tables of the Ten Commandments.
The secularist monster thus created has been an unmitigated disaster. Under secularism’s protection, Romanism has grown and prospered in America, while true Protestantism has languished since her Protestant colonial era. Under its protection, the USA has become the breeding ground of all sorts of cults and religious errors: Seventh Day Adventism, Mormonism, Jehovah’s Witnesses, the Pentecostal movement, etc. Under its protection, all sorts of moral crimes have been legalized: Sabbath desecration, adultery, sodomy, abortion, etc. Under its protection, government-financed schools and other institutions have promoted all sorts of lies, like evolution and the glorification of wicked men and nations. This secularist monster owes its birth in no small measure to the American amendment of the Westminster Standards.