These sorts of deals are the mainstay of airline/airport business these days.
The days of airports making their money out of landing fees and a healthy (£10-15) amount per passenger on top are long gone. These days a typical deal will be £2-3 per passenger (less if it is Ryanair) and no landing fees.
In return the airline pledges to bring in many more passengers, which the airport knows will spend an average of £x on parking/food/shopping etc thereby making up the shortfall.
If the airline fails to bring in the passengers it is only fair that the airport is compensated, which is why penalties are often brought into the contract.
Flybe has been operating out of NWI for 3 years so it is not as if the airport has hammered them in the first difficult months of the operation.
I know the airport MD at Norwich personally. He is one of the nicest and most honest people I have met in the industry and certainly not someone who would take unfair advantage of another party.
In my opinion it is unfair to lay the blame with the airport for this.