If just a small number of routes were responsible for the bulk of the financial losses it would be easy to drop them - and I imagine that this would have been done already
I suspect instead that many many routes each lose a modest amount of money which combined gives a large financial loss. Furthermore the revenue on each route likely more than covers the direct operating cost (fuel, navigation, airport fees and taxes) making it financially better to operate than leave the aircraft on the ground - but doesn't cover the cost of things like aircraft leases and maintenance, marketing, head office, etc.
It is much harder to turn around an airline whose whole structure is loss making and which has relatively few obvious targets. The new management will undoubtedly find some things they consider surprising but they will have plenty of hard work to reshape Flybe into a profitable company