Transit systems and roads for private vehicles provide massive benefits to society in terms of mobility. Transit systems have different (i.e. better) scaling characteristics when very many people require mobility. Also, the shared marginal cost characteristics make it a better fit for offering lifeline service to the poor.
In terms of negative externalities, society’s private vehicle fleet is a major source of polution, often the major source of polution proximate to where humans live. And then there’s the > 10x 9/11s worth of traffic fatalities that we in the United States endure each year.
So yes, we absolutely should consider the mobility benefits of roads and transit systems in context of cost recovery. As someone with a background in transportation planning, I’m inclined to think that the United States is a little too obsessed with cost recovery for transit systems, and is pretty blind to cost recovery for the public infrastructure that serves our private vehicle fleet.