Although they were victims of religious persecution in Europe, the Puritans supported the Old World theory that sanctioned it, the need for uniformity of religion in the state. Once in control in New England, they sought to break "the very neck of Schism and vile opinions."
The "business" of the first settlers, a Puritan minister recalled in 1681, "was not Toleration, but [they] were professed enemies of it."
Puritans expelled dissenters from their colonies, a fate that in 1636, befell Roger Williams and in 1638, Anne Hutchinson, America's first major female religious leader.
Expelled from Massachusetts in the dead of winter in 1636, former Puritan leader Roger Williams (1603-1683) issued an impassioned plea for freedom of conscience. He wrote, "God requireth not an uniformity of Religion to be inacted and inforced in any civill state; which inforced uniformity (sooner or later) is the greatest occasion of civill Warre, ravishing of conscience, persecution of Christ Jesus in his servants, and of hypocrisy and destruction of millions of souls." Williams later founded Rhode Island on the principle of religious freedom. He welcomed people of every shade of religious belief, even some regarded as dangerously misguided, for nothing could change his view that "forced worship stinks in God's nostrils."
Those who defied the Puritans by persistently returning to their jurisdictions risked capital punishment, a penalty imposed on four Quakers between 1659 and 1661. Those killed included Mary Dyer.
Mary Dyer (d. 1660) first ran afoul of Massachusetts authorities for supporting theological dissenter Anne Hutchinson. As a result Dyer and her family were forced to move to Rhode Island in 1638. Converted to Quakerism in England in the 1650s, Dyer returned to New England and was three times arrested and banished from Massachusetts for spreading Quaker principles. Returning to Massachusetts a fourth time, she was hanged on June 1, 1660.
Reflecting on the 17C's intolerance, Thomas Jefferson was unwilling to concede to Virginians any moral superiority to the Puritans. Beginning in 1659 Virginia enacted anti-Quaker laws, including the death penalty for refractory Quakers. Jefferson surmised that "if no capital execution took place here, as did in New England, it was not owing to the moderation of the church, or the spirit of the legislature."
In his Notes on the State of Virginia, Thomas Jefferson reflected on the religious intolerance in 17C Virginia, specifically on the anti-Quaker laws passed by the Virginia Assembly from 1659 onward. Jefferson apparently believed that it was no more than an historical accident that Quakers had not been physically punished or even executed in Virginia as they had been in Massachusetts.
See The Library of Congress.