The problem is twofold: The EMB195 lease and APD.
The EMB195 was plainly not good business and they've ended up with large leasing costs. Easing them out means more money being retained.
For them to compete with rail travel where it's a wash between flying + going through airport processing to your destination and rail travel, they need to be broadly competitively priced. Then for each adult passenger, take £13 away from the ticket price for APD going to the government. All of a sudden, there's a swathe of borderline profitable domestic routes
Worst case scenario with each aircraft with 100% loads and adult passengers only:
You are talking up to £1000 less revenue per service. If 1 aircraft is doing an average 3 return sectors each weekday, it's potentially £6.000 per day less in revenue or £1.5 million a year per aircraft. Multiply that by 70 aircraft and it's £105 million more in your coffers.
The last financial year saw them report 75% loads.
For the sake of argument, I will say 60% for adult and 15% children. Using the 6 sector day per the above, it's £611 per flight going to the government or £3600 a weekday. On an annual basis, it's £0.9 million for 1 aircraft or £63.5 million a year for the whole fleet.
Now I'm sure Flybe would much prefer to hold onto that money!