[LeanderK]

In germany, there are a lot of the "Verkehrsverbünde" and they work very well. For example, in munich there's the MVV (Münchner Verkehrsverbund), but the s-Bahn (slimiliar to BART) is operated by the Deutsche Bahn and the underground, tram and busses are operated by the MVG (the communal transit company). There are, of course, problems in most of the public-transportation networks in germany, but I don't think they are to blame. I think it's a pattern worth copying.

It even allows for some competition because you separate the provider from the system. For example, in nuremberg the provider for the s-bahn for next few years was recently auctioned off to another company after frustration with the deutsche bahn.