Germany has a general toll for all commercial vehicles heavier than 3,5 metric tons on all controlled-access highways and some federal highways. As far as I am aware, there is no instance of any sort of toll in addition to that, in particular, I am not aware of any toll that applies only to a specific section of road, such as a bridge or tunnel. The truck toll is based solely on distance driven (but not "where", only "how far"), number of axles, and the "Schadstoffklasse" (roughly "pollution class") of the motor.
There are privately operated stretches of highway in Germany, but those are paid for by other means (usually, the government, or the operator receives a fixed percentage of the above-mentioned truck toll). The operators don't collect additional tolls themselves.
There may be tolls on ferries, though, but many are "free" (meaning, they have a contract with the municipal or state government(s) on both sides of the river crossing).
Switzerland has a single flat-fee yearly toll, but I have never encountered location-specific tolls, not even at major arteries such as the Gotthard tunnel.
For me, as a German, the idea of a location-specific toll seems very strange. Roads are a vital part of infrastructure, and I expect them to be provided by the government. That's what I pay my taxes for.
The truck toll is a special case:
- Heavy commercial trucks cause a disproportionate amount of wear on the roads
- At the same time, they earn money from those roads, and even more money from well-maintained roads
- Germany is a transit country between the North Sea / Baltic Sea and the Mediterranean Sea, meaning that a disproportionate amount of trucks are not registered, owned, or operated in Germany, thus paying no taxes