When Steve Jobs famously made that comment— the “if you see a stylus, they blew it” one—it’s pretty clear that he was talking about the general use cases involving touch screens and human interaction.
Latching on to the core of an single statement in its most literal sense prevents us from growing bigger and better ideas. To come back to the comment specifically, even if Apple decided “hey, you know what… maybe we were wrong about the stylus thing” it would likely be because it took the idea, observed how the world applied it and made a judgment call.
Making the use of a stylus required in order to use a device would be wrong. That was what Jobs meant.
But using a stylus for specific uses but not be required for that use is not a bad idea. It’s simply offering additional flexibility.
I love my Fifty Three Pencil stylus which I use almost daily with the Paper app. But I wouldn’t want to use the stylus for everything.