1. Where the Government wants to subsidize some group (e.g. help the disadvantaged by giving them discounts) they should pay the fair price to the transit agency out of the budget of Welfare, not drag on the financials of the transport agency. In other words, it shouldn't be possible that the transport agency is insolvent only because most of their customers are paying next to nothing. Discussions about whether we should spend a certain sum on subsidizing the poor to ride the bus/train/etc are purely welfare budget discussions.
2. The Government should move additional money into the system when they realize an expansion of transport helps further societal goals: e.g. congestion pricing funds should help to expand transit, or the government pays part of the cost to build new rail service to reduce congestion on the roads.