Part of the explanation has to do with ideology, and how early American colonists viewed Native Americans. With a few notable exceptions, the Puritan settlers viewed Native Americans as inferior, heathen, savages. When you dehumanize another, it becomes easier to commit atrocities against them.
Part of the literature of early America that fueled anti-Indian sentiment were so-called "captivity" narratives. These were stories of white people taken captive during conflicts with Indians, who lived to write their stories. One of the most well-known of these captivity narratives was the account of Mary Rowlandson, the wife of a minister from Lancaster, Massachusetts. In 1676, she was taken captive by the Wampanoags and was ransomed after eleven weeks. Her story, A Narrative of the Captivity and Restoration of Mrs. Mary Rowlandson, was, according to the Norton Anthology of American Literature, "one of the most popular prose works of the seventeenth century, both in this country, and in England."
Before getting into the text of her account, it's important to understand the context in which it was written. In 1675, Metacomet (called Phillip by the colonists), chief of the Wampanoags, led his people on a series of attacks on the colonies, in a desperate effort to prevent further encroachment by the European settlers. The conflict, which became known as King Phillip's War, ended a year later. The Norton states, "By the time the war was over, in August of 1676, with Philip slain and his wife and children sold into slavery in the West Indies, the independent power of the New England American Indians had ended." It is important to understand this context, the systematic displacement and death of native peoples, when reading Rowlandson's account, because she makes no mention of it. When read out of context, the impression one gets of the Wampanoags is that they were indeed savage killers bent on destruction and death. When read in its proper context, however, we understand the Wampanoags as people desperately trying to defend their homeland against an invading force. Ultimately, unfortunately, the narrative that dominated at the time was Rowlandson's.
The narrative begins with an attack on Lancaster, in which many colonists are killed and Rowlandson and her children are taken captive. In her account, Rowlandson refers to the Wampanoags as "murderous wretches," "the bloody heathen," "those merciless heathen," "a company of hell-hounds," "ravenous beasts," "those barbarous creatures," "those black creatures," "this barbarous enemy," and "inhumane creatures."
After she is taken captive, Rowlandson and her children are led to various Indian settlements around New England. Because she was a Puritan, Rowlandson viewed her experiences in the context of the Bible, and employed a kind of interpretation of them known as "typology." This involves the interpretation of current events in the context of Bible stories and passages. Being a good puritan, and the wife of a minister, Rowlandson sprinkles her narrative with Bible verses, meant to mirror her own experiences. Sometimes these comparisons make sense, and other times they are baffling. When her house is destroyed and people in her town are slain by the Wampanoags, she writes,
Oh the doleful sight that now was now to behold at this house! "Come, behold the works of the Lord, what desolation he has made in the earth." (Psalm 46:8)
In one way, it makes sense to quote this verse, because the Psalm was written in the context of Israel's Babylonian captivity. Perhaps Rowlandson viewed herself as a kind of Isaraelite being taken captive by heathen Babylonians. But the verse puts the blame for the desolation not on the Wampanoags/Babylonians, but on God, which is strange.
Despite her consistent portrayal of the Indians as "merciless heathen" the actions of the Wampanoags are far more humane than those afforded to King Philip's wife and children, who were sold into slavery. Rowlandson is allowed to see her children, she is given a Bible to read, she is not made a slave, she is provided with food and shelter, she is not sexually abused, and ultimately she is ransomed back to her husband. Interestingly, as the narrative progresses, we notice less use of terms like "savage" and "heathen."
After she is returned to her family, however, she writes how she had been delivered from the "merciless and cruel heathen" into the hands of "tender-hearted and compassionate Christians." The irony here is, of course, the fact that those compassionate Christians would continue to decimate the Native Americans with increasing efficiency.