Being a monopoly does not mean that you have 100% market share. A monopoly is defined as being the producer of a product for which there are no substitutes. In order to substitute (say) a Linux distribution for Windows, it would have to read NTFS, open your document formats, participate on your Samba/Active Directory network, etc. If it cannot do those things, it is not a substitute.

Some functionality along these lines has been attained by reverse engineering, but the fact of the matter is that Microsoft does everything it can to keep competitors from producing software which interoperates with the Windows platform. In the end, what this accomplishes is to prevent competitors from developing substitutes to Windows. Thus, such behavior fits the definition of conspiring to monopolize a market.

Note that just because a substitute product to Windows *could* be developed, doesn't imply that it *would* be developed (though there is strong evidence to suggest that it would). Regardless of whether or not a substitute _would_ be developed in the case that Microsoft didn't try to prevent it from being developed, the key issue here is the fact that Microsoft is _attempting_ to prevent substitutes from being developed, through its hidden APIs, secret file formats and protocols, and software patents.