Theme (spoilers)
I think the theme of this movie was that by escaping society, Allie began to mirror its evils.
Society, whether it's awful or in decline or cruel or whatever, is largely inescapable. It's like the only salesman in town of something you need. He can spit on you, charge whatever he wants, and even beat you with the item you wish to purchase. You can either take this or try to make the item yourself, which is exceedingly difficult.
Allie didn't like this, so he went elsewhere. The first thing the movie hammers into us is that it takes a different kind of person to pick up and leave the machinery of society. However, the dark side of this personality isn't revealed until much later.
Eventually, Allie becomes an inescapable society unto himself. His family cannot leave him for the same reasons he couldn't leave society: inability to procure food and shelter, lack of safety, lack of luxury, etc. Allie provides them with all these. In return, he requires their complete loyalty in working toward his goals and tolerates no disobedience. He becomes the same monster as the society he so badly wanted to leave.
By the end of the movie, he's turned his son into the same monster society had made him into.