1) People don't drive
In US everyone drives, in fact you need one. But you see none of my friends in Japan own a car. The only people who owns one are people that are well offed. This is because owning a car in Japan is expensive (there is thing called 車検), a hassle (no parking), and getting a driver's license is long and hard. Supply is low.
2) Cash
In Japan most people still carry cash. Their preferred method of payments (in order) are: cash, Suica (debit card for train), and then credit card tied with NFC in phone that charges your phone bill. So Taxis are more convenient than Uber.
3) Part-time jobs are everywhere
You see it's very easy to get a part-time jobs. In fact most college students are doing it all the time. In US Uber looks attractive "I can drive and make money!", but in Japan it is "I just have to go to that place that dispatch part-time jobs and will make money".
4) Zoning
This is a bit similar to what the article talks about but in a different perspective. Don't forget that Japan fits in California. Each city have its own law and you need to pay a lot for each zone. My family operates in one district and have 2 competitors. Other district have its own. Each city have its own market and demand. You can't even pilot in a small region because if you drive 15 minutes you are already in another district, which you are not allowed to pickup. These zoning are strict, and japanese people know about it. It existed from the day yakuza used it as protection fees.
5) Anybody can be a taxi driver
You see its not hard to be a taxi driver if you really want to be one. These are called 個人タクシー and can operate on your own.