The hype about "on time all the time" is a well-loved-by-foreign-media myth in Japan. Yes, many trains are nearly perfect (Shinkansen, especially), but plenty of Tokyo metro lines are delayed by a few minutes during the daily rush hour crush. The point: They run so many damn trains, you can just get on another one.
Because commuters often have tight connections to make and if a train is two minutes late that can be enough to miss the next train and be late to work, which is a big no-no.