Public Transportation Monopoly

Public transportation is not all that great here in the United States, but it plays a much greater role in many European countries. Cities have a great network of bus lines, suburbs, and streetcars, different cities are connected with railroads and buses that run frequently.
Often times, this public transportation system is run by the government, at least on the local level. The particular case I am discussing here is the one of my hometown somewhere in Switzerland. It is a small city with about 36'000 people. But even a small place like that has its public transportation system, in this case there are several bus routes connecting the various neighborhoods and the city center. The bus system is run by the governemnt and there is no competition, meaning the government has a monopoly on the public transportation in the city. That means they should be able to set prices in a way that maximized profits. Now you may think that the government's goal shouldn't be to maximize profits with the public transportation system, since it is supposed to serve the citizens. You're right, so maybe they should just set prices so that they can cover the costs.
The surprising thing is that they fail to do so. Instead, they run a deficit every year that has to be filled with tax money. That doesn't make much sense. Either way the public transportation system has to be paid for. That could either happen through smart pricing strategies, or with with tax money. But only the first option implies that the organization is run efficiently and that the ones who actually benefit fro it are the ones who pay for it. Is the government not capable of running a monopoly?