I don't feel like these are a major issues today, or that they have been for some time, but back in the day I know a lot of hatred toward Windows/Microsoft stemmed from Linux users feeling slighted by the lack of support from ISVs and hardware manufacturers, the relatively immature state of Wine, and above all Microsoft's constant FUD / aggressive (and often illegal[1]) politics / lawsuit threats / etc.
Throw debacles like Silverlight, OOXML, IE, and Vista into the mix, and it's not hard to justify a lot of the resentment toward the "Evil Empire" from back then.
Today (though Microsoft had to be dragged here kicking and screaming), Microsoft actively supports open source (CodePlex), open standards (ODF is officially supported by Office), and the open Web (they're clearly genuinely trying with IE9+); on top of that, they're rolling out some pretty solid products (Kinect, Win8, MSE, WP7, Azure/AppFabric, all the random stuff MS Research does, etc.). Mind you, I still wouldn't be caught dead using Windows or any other Microsoft product, but it's nice to such an influential tech company changing for the better.
[1] http://www.wired.com/software/coolapps/news/2007/08/ooxml_vo...