Everything has to be paid for at the end of the day. Personally I think all transit (regardless of who owns the rolling stock and whether the tires are rubber or steel) should come out of the general fund because everyone benefits from a robust transit network.

Congestion is not a big deal. People willing to put up with it will put up with it. People not willing to will use the resource at different times. You will never have a system that does not get congested at peak times. The more capacity you have the less time the system will run at peak capacity (compare rush hour start/end times across cities to see this). Think of it like dumping a 5gal bucket into the sink and system capacity being the drain size. This statement applies to road, rail and everything else.