It was basically driven out of control by commerce and trade. The Pilgrims landed in the New World and immediately decided to set things up how they wanted. They tried to control things with their laws, starting immediately with the Mayflower Compact. For example you had to be a member of their church to be a citizen of Plymouth. There were laws about behavior and certain punishments. This works as long as you don't have rival communities.

Rhode Island and Connecticut were founded as refuge communities for people looking for a place to live free of the Puritans in Massachusetts Bay and Plymouth. Fishing communities in Marblehead, Nantucket, and off the coast of New Hampshire started being created right near the Puritans and were all about trade. Eventually their numbers started growing, along with their wealth and influence and the Puritans lost control. The merger of colonies also hurt their numbers as they had to accept more diverse citizens thanks to the Crown. All of this happened over the course of the 17th century.

Please see Conceived in Liberty, Vol 1 Part III The Founding of New England which describes the settlement and change in the New England states over the course of the 17th century. It is freely available.