Unfortunately commuter networks require large subsidies themselves, as everyone wants to use them for the same two hours in the morning and two hours at tea time, leaving an intensive network relatively unused for the rest of the time. Obviously you can gain some extra revenue with cheaper offers at off-peak times, and believe it or not the railway companies have quite sophisticated systems for working out how to maximise this, but the core of the problem remains.
France pays something like 13 billion a year. Totally worth it though, French trains are a delight.