I was thinking about how it could be related to the economic benefits that the settlers provided but I feel like there so many more factors to address(i.e. disease) that it's hard to pick a central one.
You're right to say economic factors played a significant role. Remember, the Puritans are settling after more than 100 years of Spanish conquest in Latin and South America and at least a century of British and French exploration of North American and the Caribbean. They knew they were going to encounter indigenous peoples and planned accordingly, bringing with them trinkets and goods for trade. This is pretty well documented and I would check out Vaughan's New England Frontier: Puritans and Indians, 1620-1675.
But, perhaps more interestingly, the Puritans were also very good at exploiting old indigenous rivalries. One of the most fascinating accounts is an attack on a Pequot village that took place during the Pequot war 1636-38. The Narragansett natives, who had supported the Puritan forces aided the attack that occurred around the Mystic area. Although the Narragansetts aided in the attack, they were so horrified by the burning of the fort with men, women, and children inside that they withdrew and many abandoned the Puritan cause. By this time, however, much of the devastation had been done and although Natives did ban together during King Philip's war of the 1760s, the significant devastation of disease and war in the decades prior and increasing number of Puritans meant that despite a good fight, the Europeans were in the clear advantage.
Jill Lapore's In the Name of War is a fantastic book about New Englanders' wars against Native people and about their non-military tactics in particular.