Trying to Understand How the Modern Never Land All Fits Together
Bear in mind that Tink is the only fairy seen in Peter Pan, and there don't seem to be any in Jake and the Never Land Pirates, either. Izzy carries around a pouch of Pixie that is only for emergencies, indicating that the dust may now be in short supply. In Jake's time, the fairies may have been all but eliminated.
Tink's worries are justified, according to Jake. Peter Pan has gone off to Earth to explore, leaving Jake and his crew in charge of protecting Never Land. It's not until Jake's Never Land Rescue that the real reason is revealed. Peter Pan has been training Jake to take over the role of Guardian of Never Land from him, and after they complete a quest to restore the Forever Tree, Pan and Tink both appear to bestow the ability to fly without pixie dust on Jake. They then leave without him, and Jake settles in with his crew as the protectors of Never Land.
That's the story of Never Land in three parts. There's an idyllic fairy Eden where Tinker Bell happily lives until she meets the guardian Peter Pan. Then there's their adventures together until the outside world comes to lure Pan back to it in the form of Wendy. Finally, there's the catharsis as Pan essentially "grows up" and leaves Never Land in the hands of a new child guardian, taking Tinker Bell, the last of the fairies, with him. Captain Hook, now an essential part of the Never Land dream, remains to give Jake his foil.
At least, that's how one dad who has watched way too many cartoons sees it.