What is long distance in Japan? A day trip from Kyoto to Hiroshima and back? Fukuoka to Kumamoto and back? Tokyo to Nagano and back? Osaka to Kanazawa and back? Tokyo to Nara and back
These are all "long" but really not that time-long distances. Shinkansen and regional trains work pretty well for these.
And yes, a lot of tourists move between the cities quite often, even some metros accept the JR pass.
I was there twice in last 3 years and for our calculation it took 5-6 return shinkansen trips to justify new jr pass price (2 weeks jr pass). And let me tell you shinkansen are experience on their own so there was no lack of will to find daytrips using them