It also happens to be the case that the lines with "that kind of schedule" are the most profitable lines. That's why they run so often.
JR East (All of Japan above Kanto) finances: http://www.jreast.co.jp/e/investor/ar/2016/pdf/ar_2016-02.pd...
According to Wikipedia Tokyo Metro made ¥63 billion in 2009.
Tokyo also has the biggest Taxi economy in the world, but as a parent said, they're more for special occasions, and cost about as much as you'd expect to pay someone to be your personal driver.
They shouldn't lose too much money or be too expensive to run, but that's the conversation to have, not how much profit they generate.
https://slatestarcodex.com/2017/02/09/considerations-on-cost...
And with how much Japan has innovated and improved their railways over the years I don't think this really applies to them. Maybe more of an American thing where we've spent $400,000,000,000 (and expected to spend $1,500,000,000,000) on a "one size fits all" fighter jet for our military that's been a complete failure in nearly every regard.
Which made me wonder whether that kind of loss is OK and can be waived off as a govt. benefit in lieu of private car ownership. I don't know how the economics would work out, but it would be interesting to see how they compare.