The simple answer to the question is that John's journey represents a rite of passage. A rite of passage is a traditional event or behavior that people engage into at a specific time in their lives. The purpose of a rite of passage is to mark a change. In this case, the change from boyhood to manhood and from child to future priest. Like his father, John had to go into a journey where he would engage in all of the traditional expected tasks that would bring him back ready and victorious.
However, although this is true, it is more complex in a post-apocalyptic novel such as By the Waters of Babylon. First, because this tribe of wild men led by John's father, and from which John the son will depart to the strange lands of the forbidden "East" are a civilization made of generations that come from the original survivors of the "Great Burning". Second, because this Great Burning refers to a nuclear bomb that blasted the city leaving the world back to primitive state.
I was taught how to read in the old books and how to make the old writings -- that was hard and took a long time. My knowledge made me happy -- it was like a fire in my heart. Most of all, I liked to hear of the Old Days and the stories of the gods. I asked myself many questions that I could not answer, but it was good to ask them. At night, I would lie awake and listen to the wind -- it seemed to me that it was the voice of the gods as they flew through the air.
Third, because in this journey, which possesses all the qualities of Native American myth and folklore, is actually a travel into the city, from one edge to the other, in search of "something". This something is made of all of the things left behind by modern humans, such as the capability of hot and cold water, artwork, music, and other entertainments. Knowing that these things exist make John a witness to something that will later become testimony; one that will forever change what the current tribe thinks of itself and its ancestors. After all, history was lost in the Great Burning, and all that was ever recorded was lost forever. Hence, John will be the first link between the old world, and the present world.