Microsoft was specifically deemed a monopoly in desktop operating systems. That was OK. The problem was that they were trying to use that to "leverage" their way into dominance on the internet, by pushing (really quite aggressively) users to use Internet Explorer, and by pushing (even bribing) websites to include "IE-only" elements. "Try to make using Netscape a jarring experience" was the way they put it.

It's that "leveraging" bit that was the problem - trying to use a monopoly in one area to destroy competition in another area.