Of course Microsoft was right about Linux. Its focus on Linux was somewhat shortsighted and narrow, as just about anyone can rise up as a competitor. Of the ones that can act as a competitor, many will even prove to be viable.
But that really wasn't the issue, was it?
The issue, and the reason Microsoft was--and continues to be--in trouble, is what it was doing about the competition. Had the then-backbone-equipped (rather than the now crony infested) federal government not taken the company to task, all of the large vendors would still be locked into anticompetitive contracts. None of them would have the opportunity to distribute any OS, save for Microsoft's, on any of their products. Without that crack to shove a wedge into, I very much doubt Linux would have made more than a small fraction of the progress it has enjoyed in the last year or so.
Ultimately, Microsoft was right about the potential for competition. Competition is what it was trying to avoid. The company was pretty good at it, too. Just like (Enron's) Andrew Fastow was good with numbers; and just like you're right in pointing out that Microsoft was right. Admittedly, I'm one of the obnoxious Mac users you hear so much about. I like seeing the inroads Linux has made. Competition is always a good thing, so long as it's fair. Microsoft wasn't a competitor. It was, and is, a dominator.