Does Terrence Malick believe in evolution? I would suggest yes. As a man who translates Heidegger I would suggest he is a learned man, a contemplative man. And The New World begs the question of where Malick stands on Heidegger, and Malick's relationship to nature. Often the director is typed as something of a naturalist, and his nature studies are what he has been known for doing, his visual poetry.
But I get the impression from The New World that Malick believes in evolution, and in man's quest for knowledge. I think he also recognizes that something is lost with each new world, that the explorer and the visited land must change, are bound to change, and yet such must be done. Which may be why I fell in some love with this film. I have only my interpretation, and it is sure to change with a repeated viewing, but what I took from the film was the idea that Malick is presenting the idea that man must evolve and move forward. It is interesting to note the lack of direct religion in Malick's films, especially in this.
This really became clear to me in the final third, in which much of the critical audience seems to have become bored. It is in Pocahontas's relationship with her second suitor, her decision to move on with her life, to move forward to me that suggests though Malick mourns the loss of innocence, he recognizes that it is something to be moved beyond. And as tragic as much of the European settlers' relationship with the Native Indian was and is, the nature of man's innate curiosity is that he had to traverse the world, to find the boundaries, to eventually travel outside of it. Manifest Destiny, in the less politicized definition, is man's innate desire to traverse, and perhaps to conquer strange new worlds, and though Malick's films have a lack of modernity(the closest he's come to filming in the present is his first film), I don't think that mean he resents the modern world. Ergo, to me the end of the film, without spoiling it, represents the tragic loss of the new world as a noble sacrifice, a worthy sacrifice to be made.
But that may just be me.