A different way of stating my point:
The THQ bundle made it possible for devs to get Humble Bundle Inc to bundle their games despite them not being drm free, cross platform. Something that was not possible before. That is a change for the worse.
It was never impossible for Humble Bundle Inc to bundle games that were not drm free or cross platform. That was always
a possibility, it just hadn't materialised yet. The THQ bundle didn't make that possible. By necessity it must have been possible prior to that bundle going live, otherwise it wouldn't have happened.
By agreeing to THQ's terms they opened up that possibility. Ofcourse it was both logically and physically possible prior to that, but first Wolfire Games and later Humble Bundle Inc refused to allow it.
By allowing it in the THQ bundle they offered developers an easy way out. Now the possibility of Windows only bundles has entered the consciousness of gamers and developers every where.
This is something that will be in their minds when making decisions on what platforms to support, developers will now at the very minimum be less likely to think along the ways of David Kalina.
HBI has removed an obstacle from some developers from going Windows only. That is a bad thing. In some cases that obstacle may have been in the only thing guranteeing a cross platform release. In fact that is pretty much what David Kalina says was the case with Tiger Style Games:
As a side note, I'll mention that there is probably zero chance there would be a Linux version of the game if not for Humble. My entire approach to building our engine was based on the goal of getting into a Bundle someday, which encouraged full cross-platform Win/Mac/Linux support.
- David Kalina
(Tiger Style Games)
"Getting in Humble to someday" will no longer provide the same kind of incentive to go cross platform, even if you have to live with the bundle your game is a part of not having "Indie" as part of its name. The THQ bundle certainly showed that that is no barrier to sucess. So even if HBI still will require cross platform support for the so called "Indie" bundles, that is a meaningless gesture so long as they offer bundles that don't have to be cross-platform.
Given its corporate and VC backing, you can be sure that HBI will want to do further Windows only bundles to replicate the success of the THQ bundle, thereby further reducing the base of potentially cross platform games.