Tokyo still needs some cars. Neither trains nor busses run 24/7. For deliveries and accessibility reasons, some people can't use the trains (at least not all of them nor all stations). In this heat we're having trouble with people, particularly the elderly, collapsing in the streets both rural and urban (my wife found an old guy collapsed last week and had to call emergency services :/)

Some of those problems could be solved (more accessible stations and carriages, more accessible busses, etc.) but there are other problems. Bus driver shortages, the number of trains running on a line already at capacity (maintenance and cargo trains run on the same tracks as commuter tracks at night when the commuter trains don't run), and the costs associated with trying to squeeze any more out. Building new lines and stations in the world's largest metro is also eye-wateringly expensive and difficult (see the depth of the Oedo line).