Flybe cannot win, either they are getting stick for having a monopoly or being told to exploit it.
With respect Rivetjoint, Vueling have not yet confirmed they are not returning next year. Also, 90 passenger may have been an average but whats the yield? If BE have to sell every seat for £40 they are not going to want to do the route as it simply would not pay for itself let alone make any profit.
Flybe have not done badly out of Southampton, and likewise Southampton and its residents have not done badly out of Flybe. It remains one of the largest stations and I am sure those responsible for routes know far more of what they are doing than any of us on here.