Their OS is still effectively a monopoly in the desktop market. And on that OS you have to make a positive action in order to use some browser other than Microsoft's preferred choice, and since most people will never bother or even know there's a difference, that leaves their own browser with an unfair market advantage based upon their OS monopoly.
And besides, Microsoft has NEVER cared about user choice. Each Windows release removes more and more options and customization capabilities. Thus complaining about users not having a choice is like tilting at windmills. Microsoft doesn't care what Mozilla thinks, they didn't make an inadvertent mistake here by changing the user's preferences during installation, they did this change on purpose.