I agree fees can not be covered by points. I have experienced this on European flights where many airports &/or countries commonly add a tax as you leave the country. To me the TrueBlue Point situation here looked like they were determining the point fee (12k) based on the entire cash fare (service fee included) even though nearly 1/2 of the fare was a service fee. I read somewhere Bermuda often has to 'rebate' airlines to fly non profitable routes to Bermuda. I wonder if JetBlue is getting one of those payments for its cash fare flights thus keeping the cash fare artificially low? Possibly JBlue is getting a 'rebate' from Bermuda on the cash fare flight but not on the flights covered by points?
In the meantime I may research a couple of the Caribbean & Mexican destinations to see if a similar price scenario exists. Probably just a small annoyance in the over all scope of things but it did get my attention. Return flight nearly halved the value of my points.