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Thomas Jefferson was a Great American, but he was also a child of his era and circumstances:

American Anti-Catholicism has its origins in the Reformation. Because the Reformation was based on an effort to correct what it perceived to be errors and excesses of the Catholic Church, it formed strong positions against the Roman clerical hierarchy and the papacy in particular. These positions were held by most Protestant spokesmen in the colonies, including those from Calvinist, Anglican and Lutheran traditions.

Because many of the British colonists, such as the Puritans and Congregationalists, were fleeing religious persecution by the Church of England, much of early American religious culture exhibited the more extreme anti-Catholic bias of these Protestant denominations. John Tracy Ellis wrote that a "universal anti-Catholic bias was brought to Jamestown in 1607 and vigorously cultivated in all the thirteen colonies from Massachusetts to Georgia."^[5] Colonial charters and laws contained specific proscriptions against Roman Catholics having any political power. Ellis noted that a common hatred of the Roman Catholic Church could bring together Anglican and Puritan clergy and laity despite their many other disagreements.
In 1642, the Colony of Virginia enacted a law prohibiting Catholic settlers. Five years later, a similar statute was enacted by the Massachusetts Bay Colony.
In 1649 the Act of Toleration was passed, where "blasphemy and the calling of opprobrious religious names" became punishable offenses, but it was repealed in 1654 and thus outlawing Catholics once again. Puritans condemned ten Catholics to death and plundered the property of the Catholic clergy. By 1692, formerly Catholic Maryland overthrew its Government, established the Church of England by law, and forced Catholics to pay heavy taxes towards its support. They were cut off from all participation in politics and additional laws were introduced that outlawed the mass, the sacraments, and Catholic schools.
In 1719, Rhode Island imposed civil restrictions on Catholics.^[6]
Pennsylvania became a safe haven for Catholic refugees from Maryland. William Penn had been harassed as a Quaker, and enacted a broad grant of religious toleration and civil rights to all who believed in God, regardless of their particular denomination. The threat of war between England and France brought about renewed suspicions against Catholics. However, the Quaker government in Pennsylvania refused to be coerced into violating their traditional policies.
Maryland passed an act of religious toleration in 1776.
Another result of anti-Catholicism in the English colonies was that the first constitution of an independent Anglican Church in the country bent over backwards to distance itself from Rome by calling itself the Protestant Episcopal Church, incorporating in its name the term, Protestant.
John Adams attended a Catholic Mass in Philadelphia one day in 1774. He praised the sermon for teaching civic duty, and enjoyed the music, but ridiculed the rituals engaged in by the parishioners.^[7] In 1788, John Jay urged the New York Legislature to require office-holders to renounce the pope and foreign authorities "in all matters ecclesiastical as well as civil," which included both the Catholic and the Anglican churches.^[8] Thomas Jefferson, referring to Europe, wrote: "History, I believe, furnishes no example of a priest-ridden people maintaining a free civil government,"^[9] and, "In every country and in every age, the priest has been hostile to liberty. He is always in alliance with the despot, abetting his abuses in return for protection to his own."^[10]