The problem is that the rules are phenomenally complex. It's easy to say that they should have just followed the rules, but IRS rules are a serious PITA to satisfy. It is quite likely that no matter what Xorg had done, the IRS could have found some error in their compliance that would enable them to revoke 501c3 status.
So the real issue is that by making it so hard to comply with the rules, regulations, and laws, it raises the question of whether the government is using "selective enforcement" to punish people, organizations, and views that they don't like. Did this happen because of a general review of nonprofits, in which case this was a simple case of good enforcement, or are "hackers" being targeted by the government (for lots of reasons, e.g. resistance to NSA monitoring), and any one of a number of technical violations would have led to the IRS' actions? In that way it is similar to the Aaron Schwartz case, and is something that should be noted, if not actively resisted.