Wow. Those are some pretty deep words... And they expect all normal teenagers to understand this stuff?
Personally, I'm the polar opposite of Pi, I don't follow any religion, I'm pretty much an atheist. But in this quote, I agree with him completely. No matter what religion you follow, even just in life, you're always going to come to a point where you doubt your beliefs. You're going to ask yourself, if what I believe in is true, and there's someone looking out for me up there, why are they letting this happen, what did I do to deserve this? No matter what, you're going to face these questions, and it will either make or break your faith.
Regardless of that, Pi also said that in order to continue your life you must move on. You have to push through the hardships and doubts. Doubting everything is not a philosophy that will help you move forwards. Doubting that your God will help you through all the problems in life, or that things all happen for a reason will lead you nowhere. I'm going to assume that he meant it because it would leave you with nothing to believe in, that it would break your spirit and soul to the point of you beginning to doubt everything about yourself.
In relation, it's like when a loved one passes away, or you break up with your partner. You go through the stages of grief. From what I know of the subject (based off a quick google) there are five stages of grief. First it starts off with denial, then anger, bargaining, depression and acceptance. From what I've read, it seems that most people get stuck on the 4th stage, depression.(big surprise there...) This is mostly because in the previous stage they attempt to regain control of their situation. When this fails, they begin to doubt their beliefs, their faith and even themselves. This is a very difficult situation to get out of and many become fixated at this point and never really move past it. Choosing to allow doubt to overcome and consume your life is akin to choosing to immobilize yourself in an attempts to get somewhere.
Now I know you're going to ask, how does this relate, in ANY way to the story? Pi gets stuck on a life boat with a TIGER! That has absolutely NOTHING to do with religion and philosophy! (No? was I close at least?)
Well well well, my dear little Hipsters of the internet, I'll gladly answer your questions. Simply keep those thick-rimmed glasses on your stylish little face and sit tight. (or stand, if sitting's too mainstream)
***SPOILER ALERT***
I want you to picture in your head, you're stranded in the middle of the Pacific Ocean in a flimsy little lifeboat with a Bengal tiger. Your entire family has perished and the only reason you survived is because you learned to swim on account of the fact that you were blessed(or cursed)with the name Piscine. Now don't go on to tell me you wouldn't begin to ask yourself, oh I don't know, WHY WAS I PUT IN THIS SITUATION? What did I do to deserve this? It would also only be natural to begin to doubt your religion, your God, maybe even go into the stages of grief on account that, y'know, your entire family is dead?
Shocking, I know.
In any case, this is only my rendition as to how all these things relate. For all I know, there could be no relation and the author just enjoys messing with young teenage brains. Heck, maybe he just wanted to write a story about a tiger on a boat but his publisher made him change it to make it more "relatable" if that's possible for a story about a tiger on a boat and a boy named Pi...

Now that, that's my kind of pie...