I see your point and agree that every bus ride is an additional cost. Keep in mind th at roads are also on-demand and generally not priced per-use. People generally pay the same for roads whether they drive a huge SUV every day that puts more stress on the road or have a small car they drive on weekends. Roads cost the same whether you use 1km to get home from work or need to travel 20km.
Roads are in fact overused and traffic is a nightmare in many cities because they are free. You could easily create a pay-per-use model for roads that charges based on usage. Instead roads are just seen as a public good used by everyone.
There's no reason why society could not treat public transportation the same way. I'm not necessarily saying it should be free. Countries with the best public transportation tend to charge something, but the goal isn't to cover the cost because transportation is seen as a public good.