One thing that contributes to cars being non-intrusive in Tokyo is just that there are many less of them than in American cities as there are many systems that de-incentivize having a car in the city.

To buy a car you need a certificate from the police attesting that you have a free parking spot of a certain size. The expressway tolls in Japan are often more expensive than gas for any long distance travel (and even the gas is expensive because there is basically no domestic oil production). The process of getting a license is much more intensive than in America. Japan has significantly more strict drunk driving laws than America (>0.03% for up to 3 years in prison, >0.05% is up to 5). Many workplaces don't allow you to drive to work (even if you could find parking) because by law their workman's comp insurance has to cover commuting and getting a policy that covers driving costs extra. There is absolutely no on-street residential parking.

All of these are deliberate policy choices that contribute to making the majority of road traffic in Tokyo be commercial and for most residents to default to some other form of transit.