My usual setting is running cost 100% and way cost 10%
On pak64 this would be impossible to play with since running costs are >>50% of the income.
There needs to be some sort of more dynamic toll. Specifically railways should cost more per train than roads because a road can see more traffic per month than a railway (many small things vs few large things). The best would be a percentage of way cost that scales based on road type. Faster roads should cost less % toll per vehicle since they should be seeing more traffic per month.
suggest the concept of road toll should go further to cover station usage. This part is especially important for sea transport. Player is paying nothing for using the pier. There is no way for public to collect the maintenance fee from those player as the sea is free to use.
I agree but the problem is tolling players fairly and efficiently. If you are a small company running busses to a public hub you should pay less toll than someone running a couple of highly profitable aircraft since you are making a lot less than them. Even though the bus player runs more convoys per month, he makes less so it should be reflected on his toll paid (since he is not making as much money from the hub).
Public service actually needs dynamic toll so it never runs in red (or only shortly does). First it should be paid a flat amount per civilian per year. This reflects tax and is used to upkeep city streets. Depending on transport percentage (mail and passengers) this may decrease over time since if 100% of passengers and mail are moved then only the transport companies are using the roads so should have to foot pretty much the entire bill. This also means that at the start players will be taxed very little with the public footing all the bill (good game progression). Then sets the player tax rate based on how much it is costing per month and how much tax can potentially bring in.
Under this model stations should suffer transfer fees based on the profit being earned and the total being spent on stop maintenance. Way usage costs are adjusted to break even with way maintenance costs and the actual toll per tile is weighted based on reasonable way traffic (a rail will have a lot higher per convoy cost than a road since roads usually can support more convoys per month as road convoys are shorter). Way maintenance is supported by citizen tax first (so using public ways at first is mostly free, going much higher late game when most passengers and mail are moved), but stop maintenance is 100% funded by usage (no free stops, people who use them have to pay).
To implement this I would recommend new metrics to stops such as "incoming" and "outgoing" profit. Toll for stop usage is then based on profit (revenue for trip - amount spent getting there) The toll rate would then be split between the two of those metrics based on weight for all public stops (so that people always pay to use them, not only in one direction to prevent exploit). Negative profit (loss) for a journey is not taxed. Profit has to be taxed for toll because otherwise, if revenue was used, unprofitable lines which barely broke even might make a loss due to a lot of infrastructure for a few very profitable lines.