The Puritans and Religious Freedom?

I have within the last week or so discovered some ancestors that immigrated to the Massachusetts Colony in during the Puritan times. My ancestor Eleanor Moulton/Phelps/Trusler, and her second husband Thomas Trusler were members of the first church of Salem Massachusetts by 1639. As an American, I was taught in school the Puritans came to the Colonies for religious freedoms, which is true, but the Puritans did not reciprocate that notion to others with different religious beliefs. On the contrary–in 1658 John Smith had helped the Salem constable arrest Quakers. Nicholas Phelps, Eleanor’s son was arrested, jailed and badly beaten for having a Quaker church meeting in his home. June 1, 1660 a Boston Quaker Mary Dyer was hung for refusing to repent her Quaker believes. About 1661 Samuel Shattuck and Nicholas Phelps sailed to England to petition parliament to help the Quakers. Returning to New England Nicholas, weakened from the voyage died not long after. The letter delivered in 1661 to King Charles I, was what it took to stop much of the Quaker persecutions.