Microsoft is not restricting whether or not their operating systems will run on the netbooks. They are only restricting whether or not a particular netbook will get a deep discount on the operating system. Netbooks are cheap enough that the full cost of Windows is significant compared to the hardware cost, so a netbook without the deep discount would need to compete with other laptops instead of other netbooks, effectively killing it.
One business reason for the discounts is market segmentation. Netbook purchasers have a different sensitivity to price than purchasers of full computers. By charging less, Microsoft may be able to sell more copies of Windows -- perhaps enough to make more total dollars than at the undiscounted price. This is also the reason why there are many different editions of Vista available at different prices.
Another business reason is to keep Linux from getting a toehold on the user desktop market. Price is the one obvious advantage of Linux, which is why it powered so many of the initial netbook offerings. By offering a steep discount only for cheap computers, Microsoft effectively defuses the threat, without cannibalizing its sales on more powerful systems.
One business reason for the discounts is market segmentation. Netbook purchasers have a different sensitivity to price than purchasers of full computers. By charging less, Microsoft may be able to sell more copies of Windows -- perhaps enough to make more total dollars than at the undiscounted price. This is also the reason why there are many different editions of Vista available at different prices.
Another business reason is to keep Linux from getting a toehold on the user desktop market. Price is the one obvious advantage of Linux, which is why it powered so many of the initial netbook offerings. By offering a steep discount only for cheap computers, Microsoft effectively defuses the threat, without cannibalizing its sales on more powerful systems.