Youth_cycler has got to the nub of the issue. The idea that Microsoft was a monopoly, or to be more accurate, was undertaking in monopolistic behaviour, came from the Internet Browser issue.
Functionally speaking, what Microsoft sought to do was to build the browser INTO the operating system, thus making all permanently-connected computers access the internet as if it were just an extension of that computer's own file system. Moreover, whenever an Office app called a web-located file, the OS (which handles such calls) would go to IE, whichever browsers were installed on the system and configured as defaults.
This led to some huge issues for users with other browsers, and in 1998/1999 if you were running Netscape on a PC, you were either an IT genius, or were experiencing a lot of incompatibilities and general annoyances.
The other key issue in the monopoly is the OEM (Original Equipment Manufacture) supply of the Operating System. MS did deals with all the major hardware vendors (Dell, Gateway, HP, Compaq etc) to supply their operating system pre-installed. Then the users were forced to accept a license agreement saying that that OS would remain on that computer, which pretty much tied up the Desktop OS market. Even now, it's difficult to get a non-MS OS pre-installed on a machine.
Finally, MS is a very acquisitive company - when someone comes out with a new trick, MS simply buys their company, with Stacker, Visio and Hotmail being key examples of this.