In 1621, Massasoit, the chief sachem of the Wampanoag nation or tribe, decided that the prudent course of action was to make an alliance with band of English religious refugees, later to be known as the Pilgrims, who had formed a small settlement which they called "New Plymouth" or "Plymouth Plantation". His people had already suffered a hideously high death rate (possibly 50% or more) from European diseases over the previous several years, and rival nations were threatening to subdue his people. The newcomers might make valuable allies. In the fall of 1621, the now-allied Wampanoags and English celebrated a feast together, which has gone down in U.S. history as the "First Thanksgiving".
In 1676, Metacom or King Philip, the middle-aged son of the long-dead Massasoit and his heir as sachem of the Wampanoag, was shot and killed in the last stages of a vicious war between the Wampanoag and several other native nations, on the one hand, and the united forces of three English colonies plus native allies, on the other. Metacom was in fact killed by a native serving as an ally of the English. Metacom/Philip's body was cut into several pieces, and his head was severed and impaled on a pike in the town of Plymouth, not far from the spot where his father and the earliest English settlers had celebrated their alliance some 55 years earlier. At least 1000 natives on the losing side, including Metacom's son, were packed onto ships to be sold as slaves in the West Indies. Thousands of other natives had either died or fled southern New England. Even those that had allied with the English got little reward other than being allowed to remain free and keep at least some of their land. It was the end of both political and cultural autonomy for the native nations in the southern part of what had now become New England.
How did something that started with at least a tentative alliance end up with the descendants of one allied group almost wiping out the descendants of their former allies as a distinct people?
European aggression and subjugation of native peoples in various non-European lands is something that happened so many times between the fifteenth century and the twentieth century that it seems inevitable that any encounter between Europeans and non-Europeans, no matter how well it started, would inevitably end in war, which would in turn usually end with the Europeans crushing their enemies. In reality, it's not quite that simple. In some cases, Europeans and natives were able to coexist relatively peacefully for a long time, and in some cases, the natives were able to beat the newcomers. Not every European was immediately inclined to look upon every non-European as an inferior. Some early encounters were genuinely friendly, although they were rarely completely free of tension. Still, it seems to me that almost all Europeans carried some important "mental baggage" that made it extremely difficult for them to treat non-Europeans as true equals for any extended length of time, and the English Pilgrim and Puritan settlers in Plymouth and later Boston and other places were no exception.
This is almost certainly a gross oversimplification, but I think that there were two assumptions shared by almost all the English settlers in what they called "New England" that made it very difficult to deal with the natives as equals. The first assumption was that Christians had a unique insight into the true purpose of life, and the true nature of both people and the entire universe, that non-Christians lacked. More specifically, the English Calvinists assumed that their particular type of Christian belief had this kind of special insight, which other versions of Christianity either lacked or had distorted, making them essentially the only true Christians. This was a pretty typical view in almost every variety of Christianity in Europe after the Reformation in the 16th century. Since religion was so central to the lives of many English settlers in New England, this set of beliefs had an even stronger effect on the way that they viewed the world than it did with many other, less intensely religious groups of Europeans who were encountering natives elsewhere.
The second assumption was that the way that their society was set up, all the rules, customs, expected behaviors, taboos, and material culture that surrounded their whole existence, was simply and objectively the best way. This is a characteristic that they shared not just with other Europeans but with just about every human culture on the face of the earth. It's probably a bad idea to say that anything is a universal trait of human cultures, because there always seem to be a few exceptions, but most cultures seem to assume that the way that they do things is the right way, the natural way, the most sensible way. What set the Europeans apart from the all the other ethnocentric cultures by the seventeenth century was simply the scope and aggressiveness of the spread of European culture. Only the Europeans were travelling around much of the known world and establishing outposts of European culture all over the place, from trading outposts to extensive settlements to full-fledged imperial territories complete with a subjugated native population (although only Spain had yet succeeded in setting up a really extensive empire, as opposed to a series of scattered outposts, by 1620).
Unlike some other European powers, the English could encounter another culture that was very different from their own without even having to leave Europe. In the early 17th century, the culture and way of life of the people in many parts of Ireland was almost as alien to most English as the culture and way of life of the natives of New England was. There were vast differences between the Irish and the Wampanoag or Massachusett, but from the point of view of the English, there were a few key points in common that made both groups "savage" and lacking in what the English considered proper, civilized living. Both native Irish and native Wampanoag lived in a society in which oral tradition, oral codes of law, and extended family and clan ties played a dominant role, while for the English written texts were becoming more authoritative than any spoken word, and extended family played a minor role in most peoples' lives compared to their immediate, nuclear family, and non-family relationships like church communities or master-servant relations. Native Irish and Native Wampanoag both cultivated some crops, but also lived a semi-migratory lifestyle, in which they would often live in different locations depending on the season. For the Irish, this moving around was primarily to find pasture for herds of domesticated animals, while for the native Americans, it was to hunt and gather different animals and plants at different times of year. The English, by contrast, practiced a more intensive form of cultivation and livestock rearing while living in the same location year-round, in sturdier and more permanent houses. Both Irish and Wampanoag had a society that emphasized bravery and skill in combat as among the most admirable traits in men. The English considered bravery admirable, but increasingly other characteristics such as self-restraint, "polite" conduct, and steady, disciplined work habits, were replacing sheer physical bravery and prowess as the marks of an ideal man.
Given that the English saw many similarities between the Irish and Native Americans, the situation in Ireland by 1620 did not bode very well for the future of Native Americans. Ireland had long been a separate kingdom that was ruled by the same individual who was King or Queen of England, but otherwise it had largely been left to its own devices. Beginning in the sixteenth century, though, the English monarchs and their tried to force Ireland to conform more closely to English political, religious, legal, and cultural norms. By the late sixteenth century, armies raised in England were battling Irish leaders who refused to submit to these impositions, and these wars were often fought mercilessly on both sides. By the early seventeenth century, both England and Scotland, now ruled by the same king, were encouraging Protestants to emigrate to Ireland and settle on lands that had been occupied by defeated Irish rebels. Some of the English settlers in Massachusetts had friends and relatives among these settlers, and in their minds they were probably undertaking a similar mission of establishing a devout and civilized community in a land that had until recently been dominated by "savage" people who knew little or nothing about true religion.
While violent conflict was not inevitable, it would have taken an exceptional amount of understanding and restraint on the part of the English in New England to overcome all of the cultural forces pushed toward a conflict with the natives sooner or later. There were some English who were inclined toward peaceful coexistence, but in the end, those with a more aggressive approach would prove more popular, and would push the course of events