> To play devils advocate, in NYC which has a massive transit network. There exists a series of private transit "companies" (sometimes just a guy with a 10 person van), that provides routes that are poorly served by the publicly run transit network.

Are they part of the regular fare structure?

No, they are typically more impromptu set ups. $5 a person, leaves Queens for Bayonne at 8am, that type of thing. Some have set pick up/ drop off locations like a normal bus. Usually cash only, under the table.