The thing is, they (the headline) say "Japan", but this only happened because it's way out in the countryside where people have a "village mentality" of helping each other out (but the trade off is that everyone sticks their nose in your business). Japan railways itself split into several separate companies upon privatization.

This would never happen in Tokyo. As much as we think of the country as being monolithic (in many ways it is), there are great differences between different regions of the country (much like any country).

Tokyo is a place where a train being 2 minutes late causes ire (and a train conductor once killed himself for a mistake as trivial as this). It's a place where if a person jumps into the train to kill themselves, many will curse under their breaths about being late to work. It's a place where if you faint in the train concourse during the morning rush hour, no one will stop to help you. It's a place where young mothers with strollers are given stinkeye on public transit. If you ask someone (in fluent Japanese) to take a photo for you, you will often be completely ignored. Tokyo is cold.

I agree with you that this story represents the good in us all. But Japan is like a black box to those who don't live there. I would caution you against idolizing it on a national level as a result of stories like this.