Possibly the worry from MS's point of view is that linux/BSD/etc.. won't be considered part of the market from a legal point of view. I mean I think it should be but I don't know what the law is.
A more likely answer though is the following. Linux threatens MS in particularly lucrative areas (servers and backend systems). Moreover, the unix software culture and software ecosystem means that few linux servers will run the various DB and backend MS software solutions.
Also, MS likely realizes the important role the developing world will play in software sales in the future and the threat that a totally free OS provides. OS X, MS likely assumed, would face too high a barrier to entry to ever get really popular (who wants to spend thousands on an OS that you find unfamiliar and are unsure if it can do what you need?) but that a free OS would be tried and gain a foothold.
Moreover, MS may think that linux's low desktop penetration means that it wouldn't provide much legal defense in the first place.