The protagonist of this story is Karana. That should make sense due to the fact that she is the easily the most central human figure in the entire story. She is the person that readers root for and care for more than any other character, and she is the character that most of the conflicts revolve around. Karana is an easy character to like. She is incredibly selfless, and readers get a really good example of this character trait when we witness her jumping off of the ship to stay on the island with her brother.
She is definitely brave to do this too because she is old enough to know that her actions are not reversible and the consequences will be tough. It is also great that Karana is not even mad at her brother, and that tells us she is incredibly quick to forgive.
As for who or what the antagonist is, that is much more open for debate. If the antagonist has to be a human, then go with Captain Orlov and the Aleuts. They are the ones that come to the island to hunt for otters and betray Chief Chowig; however, I would disagree with saying that Aleuts are the main antagonists.
Much of the novel is a man versus nature struggle. Karana struggles against the elements and the animals for her survival far more than she struggles against the Aleuts, so I would say that the main antagonist is nature and the elements. Fortunately, Karana eventually learns to live in harmony with those elements and to survive quite well.