I'm not really sure how to answer your question because I don't know what you mean. To me the reason for it doesn't really matter too much. People are opposed to improvements to our city planning and transportation networks. Call it "small mindedness", call it "having been lied to their whole lives", call it "wanting things to stay similar to what they already know", call it what you like, the fact is that they will lobby against improvements like increased density, better bike paths, and reductions in the convenience of cars.

The fact is that neither Amsterdam nor Tokyo got how they are by sheer accident. Amsterdam's case is perhaps more well-known, because they were going down exactly the same route as us in the '60s, until there was a concerted effort to reverse that (a campaign known as "Stop de Kindermoord" or "Stop the Child Murder"), and now it's one of the best cities in the world to get around in.

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).