Think you'll find that the GLA/EDI/BFS domestic routes are some of the most profitable routes for any airline.
That's partly because they are not (currently) threatened by the railway. Manchester (just over 2 hrs), Liverpool (just over 2hrs) and Birmingham (under 1hr 30m) are all now enjoying a much more reliable and faster rail service that for door to door travel will beat any airline service when you take check-in, transfers etc into account. The railway fiasco of the last decade or so has given the airlines some breathing space to be competitive, but as more money goes in and as investment in the rails begins to pay off, it's going to get messy for the airlines.
Of those three cities you mentioned, air travel is still competitive, even when you include transfers to/from city centres.
GLA - Virgin now operates this route entirely with new trains, but it still takes at least 4hrs 39mins.
EDI - GNER have the best intercity service in the country, but's more than 3 and half hours city centre to city centre.
BFS/BHD ...... er... let me just check...... the best train/ferry crossing is (by my reckoning)
11hrs 5m.
So, Northern Ireland will remain an exception until someone tries to build a bridge or dig a tunnel (hmmm) but the Scottish hubs may have to follow the northern cities of England, and concentrate more on connecting passengers rather than point to point ones.
IMHO, the regional links won't be lost, but there's no way that Manchester (for instance) will be able to sustain the number of flights to the London airports it currently has. In 20 years time, the same will probably be true for EDI and GLA, especially if this (or successive) governments bring a pollution/fuel levy into play.
*j*