King Philip's War, for a time, seriously damaged the recently arrived English colonists prospects in New England. But with their extraordinary population growth rate of about 3%/year (doubling every 25 years) they repaired all the damage, replaced their losses, rebuilt the destroyed towns and continued on with establishing new towns within a few years.

The colonist's defense of New England brought them to the attention of the British Royal government who soon tried to exploit them for their own gain. This started with the revocation of the charter of Massachusetts Bay in 1684 (enforced 1686) At the same time, an Anglican church was established in Boston in 1686, ending the Puritan monopoly on religion in Massachusetts. The legend of Connecticut's Charter Oak stems from the belief that a cavity within the tree was used in late 1687 as a hiding place for the colony's charter as Andros tried unsuccessfully to revoke their charter and take over their militia. In 1690 Plymouth's charter was not renewed and they were forced to join the Massachusetts government. The equally small colony of Rhode Island, with its largely Puritan dissident settlers, maintained its charter--mainly as a counter weight and irritant to Massachusetts. The Massachusetts General Court (their main legislative and judicial body) was brought under nominal British government control; but all members except the Royal Governor and a few of his henchmen were elected from the various towns as always.

"Thirteen towns had been laid in ashes; the wilderness was marked on every side with desolate farms and ruined homes. A thousand of the brave young men had fallen, and there was scarcely a fireside that was not a place of mourning. The public debt had risen to an enormous figure, falling most heavily on Plymouth, in proportion to population. In this colony alone the debt reached was £15,000, more, it was said, than the entire property valuation of the colony -- but this debt was paid to the last shilling."

-http://www.usahistory.info/NewEngland/King-Philips-War.html

A great start, but there's more that can be said about this topic.