Regardless of which budget each transportation comes from, there is only a finite amount total. For the Far Rockaway ferry, which cost $2.75 to the passenger, but its actual cost is closer to $30 is just appeasing to whatever constituents there. Its not like its a transit desert there, given that roughly the 1000 people that takes it per day use to take the subway to the city, now they just take the ferry because it is a more pleasant ride in the open waters.

It might sound good to have no subsidies for Citibike, but all that means is that they will only expand to areas where there will be high demand AND in close proximity to the city. They are not even entertaining the idea of expanding to areas farther away from manhattan where citibike could connect neighborhoods with their local downtowns.