In some ways, this novel is like a snapshot of life as a settler. When Fletcher leaves England, he does it for reasons of religious persecution (in that he was forbidden to marry his true love because of religious dogma). He finds a new life for himself, along with the kids of his would-be lover, Alice, who died leaving them to him. The children are named after the pillars of Christian theology: Hope and Faith.
Now throughout the novel, Hope behaves in a resilient, heroic way, and Faith isn't really in the story that much. She is raised away from the narrative, by Natives, and when the two sisters reunite, she doesn't even remember how to speak English—that's how far the two are separated. And this is the essential point of the narrative, this dilemma between world views. From Faith's point of view, we see that the Native American view of tribal honor has some merit, but we also see that Hope's more individual, destiny-oriented point of view is equally valid.
Unfortunately, any attempts for these two complicated, differing world views to come together end up thwarted. The inclusion of Native servants in white communities leaves the communities constantly spied on and ambushed. The peace talks with Magawisca and the Fletchers end up in horror when Sir Philip ambushes the meeting. Perhaps most obvious was when the settler begged a Native for some herbal cure to his illness, and when he was healed, she was tried for witchcraft.
These constant conflicts are the obstacle that Hope and Faith exist to solve. Therefore, the novel is simultaneously a story about the permanent conflict between two fatefully opposed world views, but also, it is a story about how charity, open-mindedness, and a willingness to live at peace can all be used to find hope and peace. In a word, the novel is about love, specifically love for ones enemies.