Intelligence and understanding
The novel plays around with the idea of intelligence, knowing, and understanding. There are two levels of intelligence presented (the parents are roughly equal, but their son is biologically limited by autism). But, that doesn't necessarily imply that Raj's experience is less than theirs. In fact, he is undeniably a hero in this story, because he went on a journey and came back older, wiser, more informed in an existential, emotional way.
Perhaps the novel's main point is this: There are aspects of human life that far surpass human intelligence. Therefore Raj and his parents are not unique in these ways: This is essentially a picture of life for every person.
Fate and religion
The parents are truly baffled when their severely limited, autistic son escapes their home and walks into the desert. Whether this was an overwhelming moment in his life, when he went on a "hero's journey" and encountered something divine—they can never know that for sure, but they begin to suspect that the boy had a religious encounter with a spirit, perhaps in the form of a coyote, and they wonder if it was a signal to his consciousness that he were destined to a bad fate (which is how they understand the coyote). Ultimately, this theme is more about the questions than the answers, but one thing is for sure: After returning from the desert, Raj is just different.
Existential frustration
At the end of the novel, the plot resolves, and all the characters reach the same conclusions in their existential, philosophical considerations: there is no "correct" answer. Their existential frustration does not go unresolved, however, because the value of the novel is the beauty of the ideas and story, so even to the characters, the "purpose" or point of the novel can be said this way: The experience of trying to understand reality (and failing) is itself a meaningful existential experience.
