Although TTC has a much higher cost recovery ratio (73%), it is a much larger system too. So the average Toronto taxpayer actually subsidizes transit more than the average York taxpayer. YRT has around $80 million municipal subsidy for operations, TTC over $400 million. MiWay gets around $45 million from the city.
Honestly I don't think transit should be funded so much from the property taxes in the first place. I was reading an article on the Nassua Inter-County Express (formerly MTA Long Island Bus) and it mentioned how 40% of its operating revenue comes from fares (~$45 million) and 50% comes from the state (~$55 million). So the municipality (Nassau County) only has to provide a subsidy of $4.6 million USD per year. This is a system as large as YRT too (similar ridership, similar population, similar privately operated), but it gets 4 times the funding from higher level of government than YRT does...