The logo, as you can see, is simply three tuning forks enclosed in a circle. The meaning of this mark is described on yamaha's website as such:
The three tuning forks of the Yamaha logo mark represent the cooperative relationship that links the three pillars of our business -- technology, production, and sales. They also evoke the robust vitality that has forged our reputation for sound and music the world over, a territory signified by the enclosing circle. The mark also symbolizes the three essential musical elements: melody, harmony, and rhythm.
It seems that the Yamaha mark is representative of some sort of musical trinity but Yamaha is, as we all know, not confined to the manufacturing of musical instruments but makes motorcycles and a variety of other things. They use this same mark to define their whole company though. I think that such is a wise move for them, as they had already established their mark before they moved into other realms of manufacturing. I think to change would have been, in a sense, starting over without any real visual tie to an already respected company.
I also think that is interesting that originally their logo did contain the tuning fork, but that the focus of the logo was not the tuning fork, but rather a mythical bird called a "hoo". I don't know why they chose to use such a bird as their logo but they do explain what the bird is, so I have included that explanation as well.
The hoo, a Chinese phoenix, is a mythical bird of luck, long revered in China alongside the kylin (an imaginary fiery horse), turtles, and dragons. Its appearance is said to herald the birth of an Emperor possessing saintly virtues. The front part resembles a kylin, and the rear that of a deer; the neck, a snake; the tail, a fish; the back, a turtle; the jaw, a swallow; and the beak, a chicken. In addition, the feathers of the hoo are said to feature a five-colored crest.