From a religious point of view, this family was screwed up. I mean, obviously, but there was a good reason the Puritans banished them. The father considered the puritans too lax, that they cut too many corners, so he got kicked out, because he wouldn't shut up. And instead of going to "liberal" Rhode Island, he opted to take his family separated, where Puritans feared to go.
As much as this guys seemed to care for his kids, in the end he was willing to blame innocents for his own fault. Which is the ultimate sin of "scruples" as the Catholics name it-- the sin of condemning things that are innocent. In a sense, this is a moral film which displays the results of fanaticism, of being "too" religious. But it does it honestly. Instead of condemning all religion (even all Puritan religion, which is an easy target), this film focuses on the father who destroyed his family by separating from community because he judged too much.
Although fundamentalists deny it, the major sin of the Bible is judging others. From Adam and Eve who condemned themselves for being naked (which was never an issue with God) to Jesus and Paul who condemned condemnation, the main issue of "god-fearing" humanity isn't not being pure enough, but demanding that others be more pure than they are. It's easy to see that outside of religion, but hard to keep track of inside it.
How I loved this film. The language is exquisite and it was perfect for me, who's familiar with the King James. It really feels like we're being dropped into the 17th century, and that is just wonderful.