That’s the conventional wisdom. Or at least that’s the line Morgan Stanley’s Kathryn Huberty pitched in September — when she lowered Apple’s (AAPL) rating twice in two weeks — and reiterated last week, when she earned the distinction of being the first and only mainstream Apple analyst to set a 2009 price target below $100 a share. (see here)

“PC unit growth is decelerating,” she wrote in September, “and the remaining source of growth is increasingly in the sub-$1000 market where Apple does not play.”

The only trouble with this argument, as Turley Muller of Financial Alchemist points out, is that it flies in the face of Macintosh unit sales for the first 12 months of the recession.

“Huberty claims Apple is at risk because it’s highly exposed to the premium-end, where demand has been falling,” Muller writes in an analysis posted Friday. “However, Mac unit sales grew nearly 40% for 2008, and its share in the premium segment almost doubled. Mac sales have been growing roughly 3x the market.”

Huberty, whose Mac and iPhone estimates are among the worst in the industry, has become a favorite target for Apple enthusiasts. (See Why Apple shares took a nosedive.)

But Muller may be the first to put his finger on precisely what she’s doing wrong.

“I understand why consumers aren’t paying-up for Windows PCs,” he writes. “How are HP, Dell, Acer, Toshiba, etc different from each other if they all use Intel chips, run Windows, and have many other of the same components?”

And because the PC industry is so dominated by Windows PCs, the dynamics that drive demand for Microsoft (MSFT) Windows machines are going to determine what demand for the entire industry looks like.

But, as Muller points out,

“Macs and Windows PCs are not similar product offerings. Some analysts, notably Huberty, appear to conflate the two. Macs are Windows machines, for one can install Windows OS on Mac hardware and use it just as if it were a Dell or HP. But, PCs such as Dell and HP can’t run Mac OS.”

“Therefore,” he writes, “it’s Windows PC demand that is shifting to the lower-end” (emphasis his).

Muller’s analysis suggests that Apple was right not to offer sharp Black Friday discounts and to stay out of the business of making $500 computers — the kind of “junk” Steve Jobs says Apple’s DNA won’t allow it to ship.

Even Muller concedes, however, that no company is immune to the effects of an economic downturn of this magnitude. He argues — as others have before — that once you’ve tasted the benefits of the Mac OS, it’s hard to switch back. But with money tight, buyers may be less likely to explore the high-price offerings in the Apple Store.

“The recession won’t cause cheap Windows PCs to take sales away from Macs,” he concludes. “Instead it will slow the rate that Macs take share from PCs.”

Click here to read the rest of Muller’s piece.