Anyone who really wishes to know about the Plymouth colony and their relationship with the native tribes of New England ought to understand how the conflict began after some several generations of them getting along just fine: King Philip's War.
The short story is that the emerging leader named 'Metacom' (or, 'King Philip' to the European settlers) of a formerly friendly tribe called the Wampanoag possibly had his older brother murdered so that he could assume the role of Grand Sachem. Metacom's father was Massasoit, a long time ally of the Plymouth settlers who used their trading contacts with the Pilgrims against the Pequot, Narragansett, and Mohegan -- but that all changed once the greedy and villainous Metacom took control after his father's death.
Metacom planned raids against the widely dispersed settlers and even murdered an informant who brought word of Metacom's plans to the Plymouth colony. They attacked and massacred over a dozen smaller colonies until the pilgrims managed to get the upper hand by enlisting the Wampanoag's enemies against them in an alliance. The long bloody war was finally ended when Metacom was tracked down and killed by a combined force of Indians and settlers. Most Indians thought 'good riddance' to Metacom's blood-thirst for war and resolved to let bygones be bygones.
The author over at 'Oyate.org' that you linked to presumes that all Indian tribes were as one in thought, morality, and unified by some political means -- just because they're "Native Americans". They weren't. The politics of Indian tribes on this continent were vast and intricately complicated long before white men ever stepped foot on this land. They weren't a simple childlike race of people. They demonstrated the same decency, treachery, honor, depravity, nobility, conspiracy, and morality just like every other human being on the face of the planet.
It's far too simplistic and an insult to history to separate the years of peace and conflict of that time by dividing the sides into European antagonists and Native American protagonists.