I’d understand maybe if the fly was a lot smaller then it’d be harder to hear. But I’m talking about flies like the common housefly or common fruit fly. Some make noise. Some don’t.
If the flies are a similar size then it can’t be anything to do with the speed of the wing as both species would require the same amount of lift. Other than size of the wing itself, I don’t see anything that could be different to encourage making noise.