Also something something Peter Pan. Peter is Jesus because he descended to the mortal world and then had to return to his eternally young utopia or something. Tinkerbell is the Holy Spirit who gifts Peter's disciples with flight, optimism, and the ability to speak in tongues and fight pirates. Hook is Satan, and the alligators and/or fear of clocks is his poetic self-imprisonment in the realm of sin.
The most important character, of course, is Smee, who represents the tragic archetypal sinner. He obviously has a kind heart and is not particularly talented at performing evil, but has subordinated himself to the Prince of Darkness, resulting in a self-reinforcing abusive relationship. He tries but is unable to steer his companions in sin toward a brighter future, and is ultimately dragged down with them. This continues well into the sequel until he is symbolically cast off the ship and into the depths of Hell by the Holy Spirit.
This tragedy is further compounded in that Smee appears to be the future of the wise, virtuous dwarf Doc, who appears to have simply fallen in with a bad crowd after having a crisis of faith, diet, and fashion sense.
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