EFF questions the FCC authority in the first place, and may not necessarily disagree with the Appeals Court on legal grounds. It says that Congress needs to step in and provide a truly competitive marketplace (a progressive to libertarain solution) and ban the most egregious practices. The large amount of media company consolidation, as with airlines, restricts competition.
FCC has implemented some egregious practices in the past, like try to put a broadcast flag into DRM to prohibit home Tv recording (which is accomplished legally by using provider-supplied cable boxes). But this used to be done regularly with VCR's in the 1980's, off regular broadcast.
The FCC has also interfered with neutrality in its anti-piracy efforts.
EFF is also wary of the possibility that cell phone plans could offer some but not all of the Internet. (I need it all, when I am away from home.)
EFF also crticizes "0.Facebook Mobile" (here) as encouraging fast-lane discrimination.
Update: Feb. 3
Wired has an article expressing a similar viewpoint, calling network neutrality a "Trojan horse" for future Net regulation, link, written by Berin Skoza and Geoffrey Manne,