The fundamental piece you are missing with your logic is that the negative externalities of driving a car are massive and not borne by those making the choice to drive. This leads to people choosing to drive a car at a rate that is much higher than the optimal balance for society. The best way to control for these negative externalities (risks to pedestrians, noise, pollution, congestion) is with a tax. In the US, we subsidize car usage in an eye watering and incredibly unfair way, which results in overuse of cars. If public policy were to better reflect the actual costs of driving a car, few would be able to afford it or choose it over other options
How are these externalities not borne by drivers? People with cars in nyc presumably park them on their local street that is clogged up with other neighbors cars. They drive them on nearby roads like the various expressways that cut up their own boroughs. They are very much bearing these external costs and taking advantage of their affordances. Its not like bronx drivers are protesting the various expressways that cut up their bronx neighborhood, parking cars to block the ramps or cut off access, no, they use those expressways all the same as any other driver and do benefit from the convenience and job access they bring.
Even in the first few sentances of that article I don't understand the situation they build about who pays for what. They say auto exaust is an example of an externality since car users presumably aren't affected by its ills. Here I am thinking they certainly pay for it in terms of a tradeoff between worse local air quality and convenience. Maybe some people believe things must only be paid in cash and not through time or experience.