Yes, and no. The argument (for good or ill) is that Microsoft uses its dominant position in the operating systems market to unfairly compete against applications developers. Under most anti-trust laws, leveraging a dominant position in one area to stifle competition in another is illegal. The remedy in this particular case is to allow other applications developers access to the underlying Windows operating system source code so that they can compete on a level basis with applications written for the Windows OS.
Of course, the counter-argument is that it is only because of the applications that Microsoft enjoys a dominant OS position. Unfortunately for the folks in Redmond, that didn't help them in the EU case.
Yeah, by bundling apps with the OS, such as Media Player and IE and so forth. So how does forcing open the source remedy bundling? Answer: it doesn't, obviously. It doesn't have a thing to do with the alleged crime. The EU is simply doing this because they can, and because there haven't been any operating systems of note to come out of Europe since...well, ever.