These struggles, accompanied by vigorous discussions of the rights of freeborn Englishmen, inevitably reverberated in England’s colonies, dividing them from one another and internally. Most New Englanders sided with Parliament in the Civil War of the 1640s. Some returned to England to join the Parliamentary army or take up pulpits to help create a godly commonwealth at home. But Puritan leaders were increasingly uncomfortable as the idea of religious toleration for Protestants gained favor in England. It was the revolutionary Parliament that in 1644 granted Roger Williams his charter for the Rhode Island colony he had founded after being banished from Massachusetts.
Meanwhile, a number of followers of Anne Hutchinson became Quakers, one of the sects that sprang up in England during the Civil War. Quakers held that the spirit of God dwelled within every individual, not just the elect, and that this “inner light,” rather than the Bible or teachings of the clergy, offered the surest guidance in spiritual matters. When Quakers appeared in Massachusetts, colonial officials had them whipped, fined, and banished. In 1659 and 1660, four Quakers who returned from exile were hanged, including Mary Dyer, a former disciple of Hutchinson. The treatment of Quakers gave Massachusetts a reputation in England as a hotbed of religious persecution. When Charles II, after the restoration of the monarchy in 1660, reaffirmed the Massachusetts charter, he ordered the colony to recognize the “liberty of conscience” of all Protestants. But while hangings ceased, efforts to suppress the Quakers continued, as did attacks on Baptists, whose disdain for a learned ministry also seemed to threaten Puritan beliefs.