separatists

Not only were the puritans persecuted but the separatists also.
Here is the website: http://www.usgennet.org/usa/topic/colonial/religion/history.html

The Separatists, however, did not recognize the established church, and some of them, at least, doubted that the Church of England was scriptual or that its administrations were valid. They held that any convenient number of believers might form a church and make or unmake their officers as they saw fit; that over the spiritual affairs of the church no bishop, council, synod, court, or sovereign had authority. Other churches of the same faith might no, unasked, even offer advice. Their pastors had no standing outside the parish. They were Separatists, Independents, or Congregationalists. The first independent church in England, however, was opened in Long in 1616 by the Rev. John Lothrop, afterwards the famous pioneer preacher of Barnstable, Mass., who had been won from Puritanism to Separatism by Robinson in Holland.

The Separatists, though few in number, were cruelly persecuted under Mary (1553-1558). In 1567-1569, under Elizabeth, a London congregation was thrown into prison. The men and women died of the horrors of their prisons. They were allowed while in prison neither clothing or food, and subsisted upon donations that came through their jailers. The few Puritans who were thrown into prison were mostly clergymen, whose prison life was comparatively mild. The Separatists, however, suffered not only from the persecutions of the established church, but encountered also, says Bradford, the sharp invective of the Puritans, who stirred up not only hostility at home, but even prejudiced the reformed clergy of other countries against the Separatist refugees. From 1660 to 1688 sixty thousand non-conformists and dissenters were cast into English prisons.