Contemporary audio jacks use cantilever beams, which extend into the cavity of the jack itself, and are pushed out of the way when a plug is inserted. The beams then make contact with the plug and allow data, audio, and power to be transferred. They also take up a decent amount of space; too much in Apple's opinion.
The patent mentions pogo pins, which are embedded into the cavity and extend to make contact with an inserted plug. Furthermore, the patent claims that pogo pins would "greatly reduce" the size of the audio jack "in two dimensions." Consider that the current iPod shuffle is essentially the width of its jack, and you see how it's become a limiting factor.
Do we want these things to get smaller? The shuffle already feels like a postage stamp.