I was about to reply and say, "what rock have you been living under?!" The payment terminals are simply everywhere in Tokyo; you can't miss em.
But the parent has a point: in rural and more old-fashioned areas of Japan, it's true that NFC payment systems are a bit more rare and cash is generally preferred. The exceptions are the national chain stores and convenient stores, which accept NFC payments, but for a rural resident, there might not be enough "critical" mass of stores to justify signing up.
So here we have another article that says Japan is somehow unique, homogeneous and therefore "easy" to set up NFC payments. But that's a rather flawed and tired excuse. The NFC payment systems in Japan are just as fragmented as anywhere else, with lots of mutually incompatible systems (Seven-Eleven being a prime example, accepting only their homegrown "nanaco" card). The difference is that the hardware aspects are all based on the FeLiCa standard, thus, much as different protocols can run over Ethernet, you don't need to invest in various mutually incompatible hardware sets.
People outside of Japan should follow this model too. First decide on a widely compatible communication standard (FeLiCa is a decent one and already used internationally) and then let the various billing companies fight it out.