If you read the article carefully, you'll see that it doesn't say that Apple is doomed or headed to its demise. All it's saying is that Apple missed an opportunity in the retail world by not working with big box stores.
However, other parts of the article smacked of arrogance and ignorance:
Apple’s co-founder and chief executive, can hardly be satisfied with a 3 percent share after more than 20 years of selling the Mac. Consider whether Mr. Jobs would be able to deem the iPod a success if it had gained only 3 percent of the market for portable players.
How does the writer know what Jobs' goals are? It seems pretty clear to me that Apple and Jobs don't want to dominate the market by lowering standards, they want to keep standards high and sell as many Macs as possible. If you ask me, over 3 million Macs in the first six months of this year is quite impressive, and represents good sales growth. In fact, that growth is nearly double the industry's (I think HP, the current leader, grew sales at about 14-16%, please provide correct info if wrong).
As for that "research" comany, I hardly think a survey performed over the short term is worth much. Let's see how the long term trends look, ie, number for year-over-year growth in Mac use. Then we'll have something credible to work with.
The Mac’s share of personal computers has actually edged a bit lower since Vista’s release in January, and the various flavors of Windows a bit higher, according to Net Applications, a firm in Aliso Viejo, Calif., that monitors the operating systems among visitors to 40,000 customer Web sites.
Using only customer websites isn't a great way to go. A broader indicator, like email, Google, Wikipedia, etc should also be included in this list of sites. Then a good showing of the general internet user is presented.