Autoglide:
I don't see any problem with the direct flight being dearer than the indirect - as a passenger I would be prepared to pay a bit more for the convenience of a direct flight, and I'd expect an airline to set their fare levels appropriately (i.e. more attractive service = higher fare). The issue for the short-haul carrier is that they stand to make much less for the short sector from a transferring passenger than they would from a point-to-point passenger. So the transfer passenger is not "worth nothing" but - depending on how the cost accounting is done - the short-haul connecting sector can be made to look more or less profitable.
I can therefore understand Bealine's suspicion of creative accounting. Lies, damn lies and cost accounting assumptions...