The famous apple with a bite taken out of it. Is the logo a reference to the story of Adam and Eve? Or possibly Sir Isaac Newton for the law of gravity after an apple dropped on his head? If so, then the reason would be simple as the apple in the story is the forbidden fruit that holds the power of knowledge and understanding. This story would fit the Apple company well as it represents the pursuit of knowledge while pushing the boundaries to accomplish new goals.

Another possibility for the logo creation is a bit darker. Alan Turing is credited with laying the foundations for the modern-day computer pioneering AI research and unlocking nazi war codes. 10 years after the war he laced an apple with cyanide and took a bite. Apple may have drawn up this logo as a tribute to him.

The truth is that those are just theories that Apple fans have come up with.  The logo design is meant to be simple and the bite taken out of the apple is just there for scale to differentiate the fruit from a cherry.  Overall, the design has worked out well for the company and fits well with many historical stories of fiction and nonfiction.