From Empires of the Atlantic World: Britain and Spain in America 1492-1830, by John H. Elliott (Yale U. Press, 2006), Kindle Loc. 2651-71:
The English Civil War and the king’s execution in 1649 raised, not only for Massachusetts but for all the colonies, major questions about the exact nature of their relationship with the mother country. Not only did the Civil War sharply reduce the inflow of capital and immigrants to the colonies, but it also created fundamental problems of allegiance, and posed questions about the exact location of imperial authority that would hover over the Anglo-American relationship until the coming of independence. No comparable challenge would confront the Spanish empire in America until the Napoleonic invasion brought about the collapse of royal authority in Spain in 1808. The transition from Habsburgs to Bourbons in 1700, which brought conflict to the peninsula, provoked only a few passing tremors in the American viceroyalties.
For the colonies, as for the British Isles themselves, the outbreak of the Civil War brought divided loyalties. Virginia remained faithful to the king and the Anglican establishment; Maryland briefly overthrew its government in favour of parliament, and descended between 1645 and 1647 into a period of turbulence graphically known as `the plundering time’; and many New England settlers went home in the 1640s to help establish the New Jerusalem in the mother country and join the parliamentary cause. But the absorption of the English in their own affairs during the 1640s gave the colonies even more scope than they had previously enjoyed to go their own way. Governor Winthrop of Massachusetts made the most of the opportunity to press on with the creation of new settlements and to form a Confederation of the United Colonies of New England for mutual defence. The colonies could not, however, count on being indefinitely left to their own devices. As early as 1643 the Long Parliament set up a committee under the chairmanship of the Earl of Warwick to keep an oversight over colonial affairs.
This committee, although interventionist in the West Indies in response to the activities of the royalists, and supportive of Roger Williams’s attempts to secure an independent charter for Rhode Island, was generally respectful of legitimate authority in the colonies. But its activities raised troubling questions about whether the ultimate power in colonial affairs lay with king or parliament. As early as 1621 Sir George Calvert had claimed that the king’s American possessions were his by right and were therefore not subject to the laws of parliament. This question of the ultimate location of authority became acute after the execution of the king, since several of the colonies – Virginia, Maryland, Antigua, Barbados and Bermuda – proclaimed Charles II as the new monarch on his father’s death. Parliament responded to these unwelcome colonial assertions of loyalty to the Stuarts by passing in 1650 an Act declaring that the colonies, having been `planted at the Cost, and settled by the People, and by Authority of this Nation’, were subject to the laws of the nation in parliament.
When this Act was followed in the succeeding year by the Navigation Act, it must have seemed to the colonies that the Commonwealth represented at least as grave a threat as monarchy to their cherished rights. Parliament’s bark, however, proved fiercer than its bite, and Cromwell turned out to be reluctant to interfere in colonial politics. The colonies therefore reached the Restoration of 1660 relatively unscathed. If anything, they emerged with enhanced confidence in their ability to manage their own affairs as a result of the uncertainties of the Interregnum and the impact of those uncertainties on the authority of royal and proprietary governors.