I'm not convinced of the author's details and models on fares vs taxes. The overall concept seems on track, but there's differences between direct fees (bus fare) and general funding (taxes).
The US has a long history of not understanding just how valuable and efficient shared resources are, even with the overhead of government administration. In fact, government administration is usually much more efficient than private corporation administration of the same kinds of services so we get a lot more bang for our buck.
The author does leave out the libertarians of the world. They do want every bus ride (even school busses), even police, fire, and library service paid for via contracts with the person receiving the service. It's completely infeasible and never works in practice, but they're out there.
The vast majority of public transit systems that go to a fully (or nearly fully) non-fare based model do great. People use the busses, trains, and other resources. They make better transit choices and have more money to spend in the local economy. The author hints at this, though I'm not sure they really made it clear in their writing.
To sum up: make the transit paid for by the community at large because the community at large benefits from it, even if they're not actually riding the bus. It gives us freedom as a community to have free public transit and our economies are healthier.