What is Yann Martel saying about religion in the novel? What is his true message?
I think Yann Martel is trying to illustrate his thoughts on religion through the character of Pi. In the first third of the book, the reader is walked through Pi's pre-lifeboat days. We get to see him learn about various religions and make certain beliefs and values of each religion his own. For example, Pi deeply respects Christ's selfless sacrifice. It's not Christ's divinity that interests Pi, it's Christs humanity. Pi also sees value in Islam's daily focus on prayer. He likes the open air mosques, and the brotherhood of believers that Islam so effectively develops. Lastly, Pi takes as his own Hinduism's belief in Karma. He likes thinking that the universe is conscious of people and that people's actions matter. He also sees religious value in Hinduism's belief that all of creation is connected. It's concrete and tactile in Pi's opinion.
Perhaps Martel is trying to show, through Pi, that the belief in a single religion is not necessary. Pi seems to think that each religion is its own story and rules for believers, but that each story and set of rules is basically pointing to the same thing -- live in harmony with your fellow man, the earth, and a divine being(s). To Pi, and maybe Martel, religion offers a set of stories and values that are meant to give comfort to believers, so why not take a bit from each religion to maximize comfort and security?