Walkers got him most likely. There are really only 4 possibilities of what happened to him:
#1 he survived on his own (extremely unlikely), #2 bandits found and killed him (very unlikely), #3 St. Johns caught him and used him for food (unlikely, see comments above) or #4 zombies got him (extremely likely).
I think while the bandits were assholes they wouldn't kill a young boy just for fun. Let's say they find him, do I expect them to help him, give him food, shelter etc? Most likely not. Most likely they would say "bad day for you son" and move on. Maybe even search him for food or valuable items but that'd be it. St. Johns was answered. There was no way he could survive on his own.
I think he got killed by zombies most likely, or maybe he managed to hide somwhere and died of dehydration or even starvation if he had water.