CalTrain publishes annual financial reports just like publicly listed companies. Compare fiscal 2007 with 2010. Then check out how much of their total revenue comes from subsidies vs fares.

http://www.caltrain.com/about/statsandreports/Comprehensive_...

They also provide a quarterly CapEx breakout:

http://www.caltrain.com/about/statsandreports/Quarterly_Capi...

And a breakout of ridership per station (check out page 11 of the 2010 report):

http://www.caltrain.com/about/statsandreports/Ridership.html