This is a natural, imho, extension to present speed bonus behaviour.
Presently the speed bonus is calculated on the journey.
for routes which belong to a line I would do like this: the line commercial speed as average max speed for every vehicle in a line, considering the weighted max speed of all ways the route uses (e.g. 100 tiles for the whole route, 20 of which with 160 km/h speed limit and 80 tiles with 400 km/h).
Speed bonus for that line would apply for all journeys and would be like an extra fee attached to the fare ticket, just like in RL express and high speed trains have a higher fare. The player would also see which lines produce the bonus.