There is the cultural thing, but Japanese transit is also extremely well staffed to the point where any anomalies are caught and dealt with preemptively. It's endless city rail for the most part, and there are no true gaps until you're fairly far.

During rush hour they have white gloved attendants pushing people in doors and confirming no hanging luggage or limbs, etc.

Shinkansen tracks are also often suspended or walled in.

In Tokyo you'll also often see signs apologizing for delays, but since the trains are still arriving every 2 minutes, it won't make a difference to you or your schedule whether that specific train is off schedule.

Another factor is that many lines share tracks also. This means everything needs to be on time, or else they won't mesh. Even on one line you'll have various flavors of express that overtake slower trains on the same rail at stations... meaning they have to be on time.

Of course, none of this is cheap, and neither are the tickets. It's not uncommon to find plane tickets cheaper than Shinkansen tickets. And even going 3 stations from Shibuya to Shinjuku will cost you 2 dollars on the Yamanote line. You could easily spend 10 dollars a day on a daily basis just getting around the city, and multiply that by the number of people who use the system, and it's a fortune.