I think I have figured it out. If you read the Rolling Stone article carefully, you can see that the reporter, Michael Hastings, has woven three stories together. One story is the story of General McChrystal trying to keep up morale in a tough war with his troops thinking he is too worried about civilian casualties and he is forcing them to accept too many risks as consequence. This is also the story of McChrystal feeling under time pressure from Washington. I bet this is the story Hastings pitched to McChrystal's staff and the story McChrystal thought was being reported. It is, indeed, sprinkled throughout the Rolling Stone article, and in this thread McChyrstal is pretty careful about what he says and generally comes off pretty well.
The second story is Hastings's rather tendentious reporting on what McChrystal's enemies and critics say against him -- their complaints, and their doubts about the war. While assessing reporter's motivations is always a dodgy business, I suspect that this is the story Hastings pitched to his editor. The whole thing has the feel of a hungry guy hoping to hunt a big trophy kill: taking down a four-star hero and showing that his war plan (note how Hastings describes the strategy as McChrystal's, not the president's) is fatally flawed and doomed to failure.
If those were the only two stories in the article, people would only be talking about the Rolling Stone cover. The problem for McChrystal is that there is a third story woven through the article. This is the story of McChrystal and his staff on an unexpected layover in Paris when a plane is grounded because of the volcano. This part of the story has a "weekend in Vegas" feel to it. The staff get drunk. The French get dissed. Holbrooke gets dissed. McChrystal and his staff joke about how they would answer a tough question about Vice President Biden's theories about the war. Without having access to Hastings' notes, I can't be sure, but I am willing to wager that 95 percent of the really objectionable material comes from that layover.
This third story was an accident - serendipity for the reporter and a train-wreck for McChrystal. The underlying facts are not surprising or accidental at all. Anyone who has interacted with the military, especially the special ops community from which McChrystal hails, will recognize the swagger. More to the point, we have known for over a year that Obama's national security team is plagued with serious internal bickering and that many of the principals, and especially the staffs, do not like each other. In short, it is not surprising that they talked this way. The only surprising bit is that McChrystal and his staff talked this way in front of a reporter, though less surprising when you factor in the "sailors on unexpected shore leave" aspect.
Now, of course, none of this excuses McChrystal's behavior, nor the more egregious behavior and comments of his staff. There is no "what happens in Paris, stays in Paris exception" to civil-military relations. Clearly, he allowed an unhealthy command climate to percolate and then bubble to the surface in unguarded moments. And it was reckless in the extreme to talk this way in front of a reporter who clearly was on a scalp-hunt...
A reporter on a scalp-hunt. Whatta surprise.