The first netbook, the 7" Eee PC, came with Linux only but it still became a massive hit. In other words, it doesn't look that the presence of an "inferior" and little-known operating system on this machine was a major turn-off.
But we can speculate and argue all we can, but in the end, it's all just that - speculation. Only if every single store sold *all* their nebooks with both Windows and Linux options, without giving preference and exposure to either, could we conclude that one or the other wins. As it is, in the absence of any fair competition, the 96% figure is completely meaningless.
Last week I walked into no fewer than 20 different computer stores here in Taiwan (the home of ASUS, Acer, MSI, etc), big and small, in order to buy a Linux netbook. But despite the fact that some of them displayed as many as 20 different brands and models, I found exactly 0 (zero!) netbooks shipping with Linux. Zero, nada, nothing! It just doesn't exist any more.
So yes, I believe Microsoft and its 96% figure. While people had choice between Linux and Windows, the figure was very different, but since the consumers are no longer offered a Linux option, even 96% seems low. The situation with netbooks is now exactly the same as with laptops - it's 2009 and it's still impossible to buy one without Windows pre-installed!
I always have to laugh when I read news about EU suing Microsoft for bundling a browser or a media player with Windows, but fails to see the real issue - Microsoft's complete stronghold over hardware manufacturers. ASUS, Acer, MSI, Dell, HP - they all "recommend Windows for everyday computing" on their web sites. Out of their free will, no doubt...