Oh, fun! Having read this story at least a thousand times to my daughter who selected it as her all-time favourite, this is a great question to answer. Often, we need to remember that many fairy tales can be interpreted allegorically, and they are richly symbolic archetypes that have been developed through the centuries.
The main allegorical way we could interpret this fairy tale is as follows. Firstly, there is the obvious journey from Pinocchio being a wooden puppet to his arrival at becoming a "real boy," which is of course paralleled by his disobedience and learning to become more obedient. His quest if you like is only successful when he stops being naughty and starts to behave. There is a sense in which Pinocchio therefore could stand for the child who is sinful and wants salvation, which is metaphorically refered to as becoming a real boy. Jepetto could be the loving parent, and the fairy is of course a Christ-like figure that cares for Pinocchio and grants him his "salvation" when he has shown himself to be worthy. The various trials and temptations along the way, such as the cat and the fox who steal from Pinnochio and the puppet master represent the various obstacles that prevent us from gaining our salvation.