There are many countries (or cities) in the world where you can easily get by in English beacuse almost everyone you need to / want to interact with can speak English. Amsterdam, Paris, Berlin, Stockholm are 4 the come to mind even though their native languages are Dutch, French, German, Swedish.
Japan is not one of those countries. Yes, you can survive without speaking Japanese with a lot of effort and asking friends to translate.
So it's not an unreasonable question to ask if they speak English. It's effectively asking, are they liked the 4 cities mentioned above.
I was once at a bar in Tokyo and where I met a young French woman who was thrilled to be going back to France after 6 months in Japan. She had wrongly assumed the her English would get her by like it had in many other countries who's first language was not English.