Local transportation in Germany, such as in Munich or Frankfurt, is run by transit districts or Verkehrsverbünde (sing. Verkehrsverbund, lit. traffic alliances, VV).
Fares entirely within a VV (for example, St. Goar to Cochem, which are inside the Verkehrsverbund Rhein-Mosel, VRM) will not be shown on the Bahn website. You have to go to the website of the individual VV. In addition, the Verkehrsverbünde often have lower price tickets, called Tageskarten, or day tickets, for all-day travel within the district, for one person or 2-5 people.
I am sometimes asked where these VVs are. Here is a map showing most of the Verkehrsverbünde in Germany. If you pass the mouse cursor over the VV, it might display the name. Click on the VV and it will give you a page with information, including the URL of the Verkehrsverbund's website.