To be fair, on a Microsoft Surface you would just use your pen to sign directly on the screen which is much more natural. It doesn't make any sense to me that Steve Jobs was so anti-pen, while also pushing for intuitive interaction.
Perhaps if someone added electromagnetic traction so that the screen provided some push-back to the pen tip, it would seem "natural," but as things are now, my on-screen signature is as good as a chicken scratch.
Providing a pen is an excuse to leave controls that are too small to use with your fingers. So while Windows now has a Touch mode where many controls are larger, many others which are also essential to using the system are tiny and hard or impossible to use by touch. That is what Steve Jobs was trying (successfully) to avoid.
That's how it works on an iPad. Touch/pen interfaces are terrible on the PC/Laptop form factor though. At best you gimp your desktop metaphor so it's functional with touch, at worst you have an unusable touch interface.
I think he was anti the crappy pens and digitising systems available at the time, the requirement to have a pen to use the device at all and the poor interface designs they encouraged.