The consternation is somewhat comparable to that over DTRPG. DTRPG used the word "professional" in an attempt to define their niche as different from RPGNow, which has professional companies and semipro companies, but this naturally doesn't sound complimentary to the pros who use and enjoy RPGNow.
Now we have this usage of "indie." By any reasonable definition (like those used for other fields), most game companies are "indie." WotC, White Wolf and (formerly) Decipher are examples of non-indie RPG companies, but that's pretty much it.
I took this up with Ron Edwards earlier this year. To him (as far as I understand it), "indie" means that all aspects of the game are under the authority of the creator, from production to sales. This is an odd definition and seems to mostly exist because he wanted to get Hero Wars/Heroquest into his clique, despite the fact that the setting derives from often-collaborative work in the 80s and the system is designed by Robin Laws.
(Interestingly, this makes Vampire an "indie" game, since WW is still owned by some of its original creatives. Of course, that doesn't make any sense, but what they hey
Now that Adept Press and others have decided to essentially farm out their sales, I wonder which way the goalposts will shift to further redefine "indie." Hopefully, the definition will become muddled enough to break the critical stagnation found in analyzing both business-oriented and creative-driven games, since we currently are mired in discourse-killing babble everywhere. In that vein, I hope IPR does very, very well.