What is Yann Martel's overall message about religion in Life of Pi?
I think this is largely up to the reader to decide, as there are several interpretations that are all equally viable. However I like the following one:
Religion is not as important as God. This is evidenced by the way that Pi dabbles in various religions, but they essentially mean nothing when the ship sinks and the veneer of civilization is stripped from the survivors. Pi believes that it is impossible for us to see or appreciate God's presence in a world that seems to be devoid of it, and so we need stories in order to restore meaning to the world. The officials, and most people, would prefer the story with the tiger to the cannibalistic version, meaning that most people would prefer an uplifting and fantastical story, one in which human ingenuity and perseverance over adversity triumph, rather than one which lays bare just how similar we are to animals. Religion is therefore a way in which we convince ourselves that we are more like God than beasts.