First, I invite you to check out my answer to the questionfor some perspective.
As humans, we are exceedingly flexible, and we'll tend to adapt in time to whatever the local environment requires, to help preserve our sanity and allow our brains to keep from being distressed constantly. People who ride the subways in Tokyo during rush hour are no different.
For one thing, the overcrowded train stuff happens only during a very limited period of the day, on specific express or commuter-focused lines only. Assays, when you need to be somewhere during those specific times, it beats walking! If you need to do it regularly, it beats the likely-outrageous cab fare (not to mention the amount of time either would take to get you to your destination). The rest of the time, the crowding is much less a problem, though that may seem less true in the hot sweaty summer months coming up…
Okay, that aside, why are people willing to tolerate the crowding? Simply put, people in Tokyo, and other densely-populated areas of Japan are:
- quite generally polite and respectful, which makes things easier, and
- have a different concept of "personal space" than most Westerners do.
The latter trait is certainly not exclusive to Japan… Everything is relative! But in Tokyo, where walking down a busy street often means walking in packs of a dozen or more, rather than the 4-5 you might experience regularly in New York, things just simply don't "feel crowded" until you're actually touching other people unintentionally.
As a foreigner, it was a very conscious experience for me to first experience the crush of pedestrians when I landed at Narita… And to notice, day by day, week by week, how little those same crowds affected me, and how much easier it became to see the "holes" in a crowd, if I needed to press through in a hurry without disturbing the general flow of things.
It's an acquired skill and even "taste", if you will… One borne out of necessity given the tightly-packed population. But, in many ways, I grew to vastly prefer it – it kept me far more observant in my daily routine, and made my accommodations (also very small compared to what I was used to in the US) feel downright palatial. So much so, in fact, that I can go back now and stay inwithout really noticing that I'm paying to be a giant sardine.
I know I've strayed a bit from the specifics of subway crowding, but in general our sensory inputs can be tuned up or down (just ask your garbage hauler, or a porn video editor) to suit our need for mental calm, which is one of our greatest advantages as a species.