The amazing part about the number of people who use public transport in Japan is not the staggering numbers themselves, but the ability for the system to continue working with so many users, and for it to have procedures in place that actually work smoothly for when things go wrong.

During the time of the Tohoku earthquake last year, JR and some other railway companies were criticized for their handling of matters. I am sure there were manuals being checked for what to do at that time, however, just thinking about trying to manage 4 million people or more at that time must have been very difficult.
Next time you are riding the trains consider yourself a part of the many millions in the system and enjoy.