Well, they're apparently going after the application (Bittorrent) that hogs up the most bandwidth. That's good in principal, except that it open the door to Comcast prioritizing other types of traffic.
Lets say that Comcast partners with a video site. To stifle competition, they make less bandwidth available to the users that go visit YouTube. This hurts users because it takes away their choices, and it helps Comcast because theoretically it will drive users to the "fast" sites (that they partner with and probably share advertising revenue with.)
Bittorrent is used to pirate movies, videos, music, and software. It also is used to distribute legitimate software and music. A lot of legit companies are using the technology now. Comcast artificially limiting any traffic that looks like Bittorrent means that they're hurting the pirates as well as blocking legitimate traffic.