Question

I just watched The Life of Pi. What a beautiful movie.

For everyone that has seen it, I have a question. In the end, when Pi says, "So you have heard both stories. In both of them, I lose my family, and the ship sinks. So which story do you prefer?"

The writer says, "The one with the animals."

And Pi says, "...and so it is with God."

What does that mean? Maybe it will come to me after I get some sleep, but right now, I don't get it.