With this precedent set, Youtube, Netflix, and Amazon Prime could all end up paying a Comcast Tax to remain competitive with Apple. If that happens, all of a sudden there will be way fewer video or other high bandwidth startups, unless they're lucky enough to get sufficient VC to pay off the cable companies. No new Dropboxes or Vimeos.
Also, I think this situation is fairly different than, say, Motorola manufacturing set-top boxes for cable companies.
The Apple boxes will be sold in retail stores directly to the consumer, and are an attempt by Apple to create a Netflix/Roku killer. Apple paying a Comcast tax to gain competitive advantage seems to be a pretty clear violation of what Net Neutrality was all about.