Easy: sell seats to commuters who want to get work done (currently seats are allocated to those who board closest to the beginning of the line).

Cars that you have to pay to enter, which take high-speed premium routes, get given priority by signalling systems, or just plain show up more frequently?

You could pay for Wi-Fi on trains! The system exists in Moscow and Saint Petersburg metros, you can either watch long ads or pay $2-3 monthly for ad-less Wi-Fi.

Charge property owners for the ability to own property near the transit stations.