>A noticeable effect to me of all this transit is that the car traffic on the roads usually is pretty minimal.

I don't think that's a direct effect. Within most of Tokyo, using a car just isn't a viable option for many trips for most people. Lots of people don't own a car to begin with (a parking space at your home is usually very expensive, in addition to the costs of the car itself). And if you try to use it to go somewhere, where are you going to park it? Some big stores and malls of course have parking garages, but most other places don't, or there's paid parking that's expensive. And if you're going to work on a typical day, there's probably no place to park there: companies don't provide parking for employees, they give you a pass for the transit system to get to work.

I think, overall, the reason car traffic is pretty minimal in Tokyo is because using a car just isn't very convenient most of the time, so people don't.