iPhone Hacks blog has the low down on the problems of styluses on capacitive touch screens in a post titled New Apple Patent Talks about Stylus for Capacitive Touch Screens.
The relevant bit:
According to the inventors, modern day capacitive touch sensors are not optimized to receive inputs from styluses. This is because, unlike a finger input, the small tip of the stylus can often get in contact with a region that is in between adjacent touch sensors hindering normal usage. In order to solve this, the stylus shall come with a conductive disk that will enable sufficient electrical interaction with at least one of the adjacent touch sensors.