If Flymaybe do decide to operate other routes from Manston. it'll be on their terms.
It' my understanding that new routes from new airports (or even ones they've operated from previously, or currently) are on a sliding scale. i.e at a place like Manston, it will be strictly no landing fees or passenger taxes charged to the airline for an unspecified period of time.
This used to be, on average, around 3 months, but I've recently heard of a major airport in the north of England offering a major operator (bigger than Flybe), 18 months on those terms.
It's then up to the airport to make money via passenger throughput in the terminal.
It's difficult to see how Manston are even going to cover their costs, never mind making a profit.