The motivations, religion and economies of the two regions were different from the very beginning. The Chesapeake colonies were Royal colonies and Single Proprietorship Maryland, all cash crop economies based largely on tobacco farming and slave labor. The main motivation for Virginia and the Carolinas being settled was simple economic profit.
In New England, you had religious diversity and a subsistence economy with few actual social ties to Mother England. As their economy would not sustain cash crops (poor soils, the wrong climate and lack of a real river system), they developed into merchants, yeoman farmers and fisherman that did not have such sustained trade with Great Britain. Their religious discrimination in England had prompted them to come to the colonies and establish havens for Puritans and Quakers, as well as others, and many wished to have little to do with the King or his Anglican Chesapeake colonies.
Finally, there was a considerable physical distance between the two regions and no real road system by 1700, so they were socially isolated from each other except for the port cities.