Extending their cost advantage
Tim Cook is doing a great job of procuring top-quality components at low cost. Using proprietary best-of-class processes have given and will continue to give Apple advantages in cost and quality. The Anobit MSP flash memory technology, Sharp IGZO LCD and next-gen OLED panel technologies, "integrated embedded battery" technology, and MacBook aluminum milling machine technology are just a few examples.
By owning the technology and the means of production, Apple can ensure component supply, keep their costs down, and prevent competitors from copying their processes and designs. And yes, Apple has patented all of their innovations. That's what patents are for: protecting innovation.