I don't think you're factoring in the weather: Tokyo is incredibly hot and humid in Summer (even more than Singapore, but there it's like that all year round), has a long rainy season in late-spring/early-summer and regular typhoons in late-summer/early-fall. Basically, for more than half of the year you're severely pondering the convenience of taking a cab over walking in the heat/rain.

Even then, the vast majority of people taking taxis regularly are business people going to and from business meetings and expensing it away, as evidenced by the heavily targeted ads for BtoB SaaS playing on the screens in the back of Tokyo taxis.