How did the turmoil of the english civil war affect england's colonial enterprises?

During the English civil war, England left the colonies alone for a period of twenty years. While the English were fighting the colonies were free and essentially got away with anything, this included not obeying the Navigation Act of 1651.

Commerce in tobacco and materials used in shipping attached the colonies economically to England, the politics and religion also tied the colonies to England, but in general the English left the colonies to their own means. The English civil war demanded the colonists in America to review their place within the English domain; the colonies that were consider old colonies such as Virginia and Maryland supported the crown, while newer colonies like Massachusetts Bay tendered to favor the English Parliament. Nevertheless, during the war all colonies remained neutral, fearing that supporting either side could implicate them in the war.

Charles I's death penalty and execution in 1649 changed that neutrality. Six colonies, including Virginia, declared their loyalty to the dead monarch's son Charles II. The English Parliament replied with and Act in 1650, which levelled an economic imposition forcing them to accept the Parliaments authority.  The Navigation Act of 1651 followed this imposition, pressuring the merchants in every colony to ship goods directly to England in England ships.  

d: social contract theory