You are leaving out a lot.  The US gave the bonds from Puerto Rico special tax status and had prevented the territory from ever defaulting on their debts.  They also gave special tax breaks to companies that located there (and then took them away).  There is also the problem of brain drain where anyone from the territory can move to the mainland for a much higher income and millions have.  
At this point we have an obligation since they are part of the US.  If you want to get rid of that obligation in the future then it becomes time to negotiate their independence.  What won't work is what people seem to be suggesting here, considering them second class citizens.  If that would work then I think Houston should be treated pretty much the same way since they have known for decades that they were living in a flood basin and just kept building.  If fact, the most coastal residents should be on their own since it is obvious they are all just one storm away from tragedy.