Story is totally pro-atheism
It shows religions (and believing in Gods) are only wishful thinking to hide from the brutality of the material world.
"ADULT PI :So which story do you prefer?
WRITER: The story with the tiger. That's
the better story.
ADULT PI: Thank you. And so it goes with God."
With the storm representing Christianity and the island representing Islam (Iam quite sure there is a metaphor of Hinduism as well but iam not familiar with that ), the movie (or novel) views religions negatively with a critical eye and totally dismisses them.
Iam a muslim myself, so though i don't like the message of the novel, it is still an excellent thought provoking one.