FCS is actually a very expensive level to play at in that the costs to have a program at that level (scholarships, salaries, facilities etc etc) approximate that of the FBS-level but with nowhere near the $$$ (TV, Bowls, attendance) schools at the FBS can bring in.
A big problem for UConn (and BC is starting to see this too) is that FBS-level football just isn't in the Norteast football-fan DNA in general. The success of the Pats over the past 20 years has sucked a lot of the football oxygen out of "casual fans" in New England who might go to an FBS game at BC or UConn in the past.
UConn football may have some success moving forward but E. Hartford is never going to be a destination-spot like State College, PA, Ann Arbor etc etc