> My town was far enough out that the cost was slightly cheaper to drive (before the congestion fee)

Aside from culture, this is another aspect which they touch on in the article. Japan doesn't have public parking. You're only allowed to buy a car if you have access to a parking spot. Tokyo is full of lots but they're all paid lots that charge in 30-60 min increments. There's also a lot of congestion zones in Tokyo which make driving in the city very expensive. Companies that do deliveries in the city often have a company car (or fleet of such) which lets them drive to destinations.

Overnight workers who do spend significant times at work before/after the trains stop do drive in. Most Japanese families in Tokyo live in suburbs surrounding the city and will walk, bike, or drive to a nearest train station to commute in.