The new Timers feature we are releasing soon should, I think, take care of this. We typically know how many hours of fuel are on board, so you can setup a custom countdown timer, with the "Only in Flight" option checked, and voila, a fuel remaining time.
Of course a smarter fuel timer might track your airspeed and climb/descent, and adjust the timer accordingly. But as the iFly only knows about ground speed, not airspeed, this simply wouldn't work.
-Walter