It seems simple enough: the Puritans believed Quakers were heretics. In fact, anyone who was not an Anglican was a heretic, including Catholics, Lutherans, Anabaptists, Antinomians, Quakers, Ranters… in short, anyone who was not Anglican.
Heretics were seen as blasphemers who put barriers in the way of salvation; they were also considered traitors to their country because they did not belong to the official state religion. This was true throughout Europe in the century following the Protestant Reformation: whatever religion the king chose became the official state religion of his country, and all other religions or sects were made illegal. In fact, the Puritans had left England because they had been considered heretics there, and had been persecuted by the government. Technically, they were not heretics because they did not leave the official Church of England (the Anglican Church), but their demands for big changes to that church made them outsiders. It was enough to get the anti-Puritan Archbishop of Canterbury, William Laud, to launch a campaign of persecution against them.
So when Quakers showed up in Boston in the 1650s, it’s no surprise they were persecuted. Puritan Congregationalism was the official—and only—religion of New England. Like every other state they knew of in Europe, the Puritans enforced a state religion that it was treason to oppose. But it wasn’t just about their religion. The persecution of Quakers was also part of the Puritans’ determination to rule themselves, independent of England.
The Puritans who had remained in England during the Great Migration to America of the 1630s drifted apart from their New England brethren. They were more inclined to allow toleration of other professions of Christian faith. The impossibility of reforming, or purifying, the Anglican Church in England was slowly rejected in favor of the much more doable task of simply confirming England as a Protestant nation by allowing any and all Protestants to worship relatively freely. The English Puritans also supported presbyterianism, a system in which the state governs the church and appoints a hierarchy to oversee all churches.
To the New England Puritans, both toleration and presbyterianism were unacceptable. They had spent painstaking years establishing a system of church government called the New England Way that was based on the independence and power of the individual congregation. The state in Massachusetts did not appoint clergy, nor was there one over-arching body that regulated churches. Each church was a sovereign unit. And only one church was tolerated in Massachusetts: the Puritan, or Congregational church (which was, to them, the purified Anglican church in America).
Worried that the English government would try to force its new rules of toleration and presbyterianism on them, the Puritans of Massachusetts made preparations to fight for their independence. They elected their own governor and General Court (a combined legislature and judiciary). They built many forts to protect their harbor and drilled their militia men regularly. And they continued to persecute Quakers, who, determined to bring their version of the Gospel to New England, continued to trespass into Boston despite the harsh and often cruel punishments they knew they would receive.
Those Quakers were not meek and mild innocents who just wanted to talk. They were as righteous a group of zealots as most Puritans, and when they entered a Massachusetts town they tried to wreak maximum havoc: bursting into church services, yelling in the streets, banging pots and pans together, and even stripping off their clothes (to show their lack of attachment to worldly things). The Puritans reacted with vehement rejection, and submitted Quakers who would not heed the warnings to leave and never return to terrible punishments. Boring holes through their tongues was just one of these.
The Quakers had no one to turn to for help until 1660, when the monarchy in England was restored, and Charles II came to the throne. One of his first acts as king was to send a letter to the governor of the Massachusetts Bay Colony (the most powerful New England colony) ordering the persecutions of Quakers to stop. According to the “King’s Missive,” any Quaker accused of breaking the law in Massachusetts should be sent unharmed to England for trial.
Charles II issued his order for two reasons. First, he was a Catholic sympathizer, and Quakers and Catholics were about the only groups who found absolutely no acceptance in England. If Charles could win tolerance for Quakers, perhaps he could win eventual tolerance for Catholics. Second, he cast a dark eye on Massachusetts’ independence. Disgruntled ex-colonists who left New England to return home told Charles the Puritans were rebels. It didn’t help that two of the judges who had condemned his father, Charles I, to death had fled to New Haven and received a hero’s welcome there.
The new king put Massachusetts in a bind: if they stopped persecuting Quakers, and sent them to England for trial, that lessened the authority of their locally elected General Court. If they gave up the authority to prosecute Quakers, what other bit of their independence would they have to give up next? It was a slippery slope leading to direct English rule. But on the other hand, if they did not stop persecuting Quakers, they would be in violation of the King’s law, traitors, and would be immediately occupied by English soldiers and forced to accept a royal governor (rather than their own elected governor). Massachusetts made its choice: they would stave off English rule as long as possible rather than call down instant English rule on themselves. Slowly the persecution of Quakers came to an end.
They would win many small battles with the king and maintain their independence until 1691, when Massachusetts’ charter was revoked and the powerful colony came at last under direct rule from England. By that time, toleration was the rule even in New England, and Quakers were no longer a dangerous and radical sect but commonplace members of society. But resentment of English rule did not die out amongst New Englanders; less than 100 years later, the descendants of the Puritans would buck off English rule in America for good.
(For more on the Puritans and Quakers, their differences, and their battles, see Puritans v. Quakers in the battle for our sympathies.)