They were arrested and treated harshly because they didn't belong to the Church of England.
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After the English Restoration, where the Puritans were eventually hated by the citizens, the Puritans went to the Massachusetts, one of the 13 colonies. The Puritans went there because they wanted to escape a religious persecution in Europe. Also, Massachusetts was a free land that the Puritans weren't going to be judged or have a religious persecution.
1620 in Mass when they landed they wrote the Mayflower Compact and this was their government.
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The Mayflower Compact stated that the Puritans would follow the rules of the government. They didn't arrive where they originally intended so the rules of England did not apply. The Compact was created to assure the half of the ship's passengers who were not Puritans that the government of the colony would be elected, not imposed on them.