The primary fixed cost for prototype railroads is the cost of their track and buildings. Some of the cost for track is variable because it requires more repair under high use but to keep it simple I look at track and buildings as fixed cost.

So we arrive at what seems to be a big problem. A management environment is not very realistic if we do not have competition and the traditional way US railroads compete is with each railroad running their own track (might not be that smart when you think about it). On a model railroad we have trouble finding room for one railroad's track and we sure do not have the means to add competing tracks. Looking to the prototype there are several locations where two or more railroads share the same track and split the costs so you can find a prototype or two for this.  In fact I expect two railroads using the same track happens in more places then you would expect if you look. In my case with my location in Middle Earth I can change the rules so I will have the government own all the railroad track and the railroad company pays fees for a train license that would equal their portion of fixed cost of the track for each train they want to be able to run. Taking the road bed model from the trucking industry works just fine for competing railroads on one set of tracks.

License cost for a train would depend on a time table train vs an extra train. A time table license would have a first class (more money of course) or second class level and would cover a six session period first come first serve. If the train does not run no refund from the government but after two sessions in a row of the train not running the license is lost (I guess the government guys just don't care about people with troubles)!  An extra train license would be paid by session and the train would run as third class.  Because my main line is short I expect to need a west bound block of extras in the morning and a east bound block of extras in the evening to get any extras a chance to move.

Have you wondered about the yards and terminals yet? For yards and terminals we can borrow from the airline industry. A fee to use a terminal or yard with the yard crews paid and managed by the provider of the yard or terminal. The cost of the dispatcher would be like the cost of air traffic controllers. The yard fee would be by car and the terminal fee would be by passenger or express train and would be part of variable cost.

The equipment is an area where I think we have to bother with fix cost and variable cost. There several fixed costs to owning equipment and I have it simplified as one computed value that is available before equipment is purchased that is a cost per session that never changes. The variable cost will be created when the equipment is used. Crews will be variable cost and will not have to be paid if you don't use them so they are not a fixed cost.

So in the end we have very simple fixed costs. You have a license fee for each train you want to run and a fixed cost for each locomotive and car that you own.