When you compare something like St Albans to London, with 12-car 700s running full loads of passengers into London with something like Reading to Basingstoke or the North Downs Line using 3-car units at less than crush load on a half hourly basis it seems obvious that the first will make money for the railway and the latter needs revenue support, even if the trains are full to the point of all seats occupied.
The advantage of the railway is where it can move large numbers of people. If they were run commercially I do not think that lines like Reading to Basingstoke or the North Downs Line, on their own, could justify new trains without external funding.
Back in the early 1990s, Network South East was fortunate that it could extend its Thames Line order for Turbo units by one extra 2-car unit to cover Reading to Basingstoke, with the other covered by the existing order, and then, in the light of a growth build on the Chiltern line and lower passenger numbers after the early 1990s recession, free up seven units for the North Downs Line.
Clearly they aren't the biggest basket cases on the railway but neither are they money spinners. I guess that some of the operational cost of Reading to Basingstoke as a route is covered by freight which helps. North Downs Line much less clear.