The fact that it's a natural monopoly makes it susceptible to a lot of the same problems as a government, but making it an independent entity actually mitigates them somewhat by reducing the size of the bureaucracy. One of the big problems with elected governments is that the Republican wants to install a corrupt transportation board and the Democrat wants to install a corrupt school board and you have to pick your poison. If you get to elect the directors responsible for local transportation separately from the directors responsible for local schools, that doesn't happen as much.
It also helps quite a lot to move as much of the spending as possible to as local a level as possible, because then you don't get wasteful pork motivated by a desire for inter-region wealth transfers.