It's more complex

First thing the distance between the stations. second the time you need to get there. (100km/h are 1024 tiles/month) that's the speed bonus. It's only with cargo and the mean speed (because time to get there). So the calc values when you go to Vehicle-details are only if you have the speed all the time and stop-go not only in one direction at the direct way per tile.
Don't know if the time is running if the first load is done (like in Chris Sawyers Locomotions) or after you start driving

Thats the cause why Trucks are better at short distance because they have higher speed gain (mean speed at short distance), whereas the train wasn't at full speed before hitting the station (only by high speed bonus cargo)

Interesting- thanks for the details! I ran some tests to try to confirm that it's using the average speed, and it seems to be true. I wish I knew this earlier, I would have set up my lines very differently. Also, I wish this mechanic was more clearly documented somewhere (unless there's a place I'm not aware of).

The speed bonus is not based on the real speed, but on the possible speed going over all tiles. So it takes into account speed limits and overloading, but not congestions and waiting in front of red signals/traffic lights. Hence, for a given route, the speed bonus will be the same for each run. Long trains are bad at short distances, because the actual length travelled (and hence charged) is shorter by half the station lengths.

It's a relief that it doesn't take congestion into account. Is this calculation documented somewhere? Or do you know where in the source code I could reference this?

You can find it in simvehicle.cc line 1254 ff, in the routine sint64 vehicle_t::calc_revenue(const koord3d& start, const koord3d& end) const

Awesome- thanks!