The Rail Pass is valid on all train services operated by JR (Japan Rail Railways)
It is not valid on other privately-operated railways.
Examples of private railways:
Keisei Express service from Narita airport to Tokyo
Nankai Express service from KIX airport to Namba (Osaka)
Odakyu Express service from Shinjuku(Tokyo) to Hakone
But for all the above, there is also a JR service – which may be slower or less frequent – for which the Rail Pass can be used.
There are a couple of exceptional cases where the Rail Pass cannot be used, even though the services are operated by JR:
“Nozomi” bullet trains on the Tokyo-Kyoto-Osaka (Tokaido) line
“Mizuho” bullet trains on the Kyushu Shinkansen line