The people who are upset that the've drifted out of the indie sphere don't really have a case but I can't blame them for being upset.
Weeell, a few of the comments on that Ars article make a good point I think: they shouldn't have kept the "Humble Bundle" branding if they were going to diverge so heavily from the original premise. While TA's correct that they've had "Humble eBook Bundle", "Humble Music Bundle", "Humble Bundle for Android", et al, they've generally stuck to the "Indie" part of the name even when they weren't using it. (And while Shinra's correct that there have been other individual contributions that weren't independent, I can't remember an occasion when the ENTIRE BUNDLE was from a major publisher.)
Not-So-Humble Bundle could have worked. Or just the "THQ Bundle". I'm not even saying don't use the humblebundle.com domain name, just, you know, change the banner a bit more.
(In fairness, the word "Indie" isn't anywhere in the domain name or the banner, and they're not calling this Humble Bundle 7 or anything. I think semantics are important, but it IS a semantic issue.)
The people who are upset that HIB has dropped its stance on DRM have a case. Not only are we tossing the "see kids this works" aspect out the windah, but the free-distribution model is really the only way the pay-what-you-want model ever made any sense. It's a subtle shift from an open economy to a closed one with really, really bad negotiation practices.
Yeah, I have a problem with that. It is a very bad precedent, and, seeing as it's made a million dollars in one day, we can pretty much guarantee it WILL set a precedent.