Unfortunately APD has seriously effected shirt haul U2 flights which compete with roads and rail. For example, NCL-STN was four daily. That route went about 5 years ago. Now there is an E135 which barely half fills on the once a day flight. BRS is also down to flights where they can attract a good yield and turn a profit.
On a domestic flight (particularly intra England) £16 APD is a significant portion of the ticket. You're limited as to how much you can charge as driving is probably cheaper and door to door there's not much in it time wise. The trains are pretty much hourly too.
The same cannot be said for NCL BFS where there is no practical alternative. Your yields will be better as people are prepared to pay more.
I'm sure they're doing the best they can. I know some of the BRS flights are done by BRS jets assuming they are keeping NCL based jets to operate higher yield routes..