It shouldn’t be run as a business. It should be run as a service. Who cares if there’s a shortfall. That’s the cost of ensuring citizens have cheap, efficient, reliable, green ways of commuting.
In my opinion, the cost of facing overcrowding shouldn’t be coming from fares at all. If you have a better way for people in a city to commute, why charge people who are using that better way more? That just dissuades them from using it.
Tax 101: Tax the people who are choosing unhealthy options, and use the tax to pay for healthy options.