From Tony Chambers’ interview with Jony Ive on the Apple Pencil:

I think there’s a potential to confuse the role of the Pencil with the role of your finger in iOS, and I actually think it’s very clear the Pencil is for making marks, and the finger is a fundamental point of interface for everything within the operating system. And those are two very different activities with two very different goals.

So we are very clear in our own minds that this will absolutely not replace the finger as a point of interface. But it is, and I don’t think anybody would argue, a far better tool than your finger when your focus becomes exclusively making marks. The traditional pencil could have been replaced by a dish of powdered charcoal, which you dipped your finger into to make marks with. And that didn’t happen.

The interview also has some interesting thoughts by Ive on avoiding to model the Pencil after specific physical tools.