The first time we meet him, our poor buddy the Pirate is a target for one of Pilon's scams. Everybody knows he makes a quarter a day and never spends a penny, so the logical conclusion is that he's got a stash of quarters hidden somewhere, and Pilon aims to find it.
However, as Pilon and the rest of Danny's friends get to know the Pirate, they realize that the stash is beyond their reach: it's totally dedicated to Saint Francis.
That means the stash is off limits to the good Catholic friends: "The hoard was aimed at a gold candlestick, and this potential candlestick was the property of San Francisco de Assisi. It is far worse to defraud a saint than it is to take liberties with the law." (12.2) The friends see that the quarters aren't just boring old money; they're holy. Who's gonna steal from a saint?
Because the friends change their attitude toward the stash, it takes on a life of its own, becoming a symbol for their friendship. How do we know? Well, for one thing, the narrator conveniently tells us so:
The bag of money had become the symbolic center of the friendship, the point of trust about which the fraternity revolved. They were proud of the money, proud that they had never tampered with it. About the guardianship of the Pirate's money there had grown a structure of self-respect and not a little complacency. It is a fine thing for a man to be trusted. (12.2)
The Pirate's stash of 1,000 quarters (for you math whizzes, that's $250—a lot of money back in the 1930s—and the product of almost three years of work for the Pirate) become a symbol for the friendship among these guys because it gives them a way to prove their trustworthiness and show their trust in each other.
The friends know that none of them will steal (except for Big Joe, who gets the beating of his life for it and gives the money back, anyway), which strengthens their friendship—and even, if you look at it in a certain way, makes it kind of holy. Whatever else these guys may get up to, this stash represents something bigger and better in their lives.