Well fundamentally, if Microsoft controls the only viable platform for your business to run it's applications on then they control your business.
Look at what happened to Novell. Microsoft is able to provide tight integration between Windows Desktop, Office, and Active Directory and make it all work by 'default'. This required very little skill and was cheap to setup and get working. Novell on the other hand required very experienced people to setup the same thing and was much more expensive to deploy.
So Novell lost hard and now AD is the defacto standard method for managing corporate desktop environments.
Microsoft controlled the only viable platform for deploying Novell's software so Novell could not compete, even though their solutions were technically superior in most respects.
And it's the same thing with WWW. Microsoft, for the longest time, controls the only viable platform for reaching the majority of users out there. That's why it's a pipe dream that will never come true that web applications on browsers will displace the importance of Windows.
Microsoft has to much control over your platform.
Witness the debates over the <video> tag and such. Apple may be acting like a huge dick and throwing a wrench into the entire thing, but fundamentally everybody knows it's mostly irrelevant unless Microsoft decides to add video tag support to IE, which they won't do.
If they don't do that then turns something that exceptionally trivial to deploy* and turns into a major headache were you need to support the current way of doing things + the new video-tag way.
*(streaming video via video tag is so cheap and easy it is just massively blows away any competition. Try it sometime, it's laughable how simple video tag makes things. To RTSP server, no flash BS, no special software, no Apache modules, no nothing. Just drop the video file on your server and point at it like it was a jpeg image.)
And even if Chrome and Firefox do overthrow IE as the dominate browser it is only one small step. Microsoft still controls the platforms that they run on and will still be able to limit the viability of it and push their own solutions forward.