It's worth noting that mismanagement (I don't think there has been significant mismanagement, but it's up for debate) is not the main cause of the requirement for cutbacks. The main issue is that CalTrain is no-one's responsibility in particular. Almost half of CalTrain's funding comes from ticket sales, which is not the normal pattern for public transit. The other local transportation agencies (GGT, SamTrans, and BART) have dedicated sponsors from municipal governments. CalTrain, as the name implies, used to be state-funded. A couple of decades back, CalTrans, the state agency, stopped funding it, and municipal governments stepped in. However, their funding has always fluctuated - and this year, has pretty much evaporated.

Remember, public transportation runs the way it does because it's a public good - it is pretty much by definition something that the market is bad at providing, but which people need anyhow. If CalTrain had to survive off of ticket revenue alone, it would cost more than twice as much to ride, and would thus exclude some riders, harming revenues further. On top of this, CalTrain relieves traffic - it provides a significant positive externality instead of capturing value. Government subsidies to public transportation agencies address this externality.

CalTrain is dying because of the tragedy of the commons: a great many people can benefit from it (traffic, air quality) without paying for it, and will resist any attempt to require that they contribute to it. This is the situation that many, many public agencies are in.