Nice and easy way to do this is to set the fare per tile, so a journey of 3 tiles would cost $/£/€ (insert amount here), and a journey of 500 tiles would cost $/£/€ (insert amount here).
The reasoning behind it is that you have company A running from A to B (10 tiles) and B to C (15 tiles), and they have a competitpr that runs from B to C, The vehicles being used will collect any cargo waiting, so Company A will get to B and have no cargo waiting, and will make a loss on the journey from B - C.
But, if you had fares, Company A could set a fare of £1 per tile, and Company B £2 per tile, This makes Company A more attractive, meaning that Company B now has no passengers, even though it is a shorter journey it's fare is too high.
It could add a great level of competition to the game, as currently once you have set up the routes and added vehicles you can leave a game for a few hours, whereas with fares it would require great skill to get the correct fare against the running costs of a vehicle.
I don't see this making it in to any of the major releases, but if it could be integreted into CargoD(e/i)st or Infrastructure Sharing then it would make me smile.
In order to survive as a small company, you would need to be very flexible, and change routes when the others try to squeeze you out. That is not possible with trains, but maybe with the other transport forms. Subsidies, as welshdragon mentioned, is also a good example of an opportunity for a small company. In practice though, I think this mode will only work well when players are quite comparable, and start simultaneously. Then it can be exciting, as you may actually loose. Some really good players may find it challenging to start late though.
