In order to "win" the browser wars (IE at one time had a VERY small user base on the internet) MS hooked, attached, embedded, connected, installed and merged IE into Windows. This allowed MS to come up with cool technologies and new ways of doing things that the other browsers couldn't/wouldn't. They defined their own standards and because of integration with Windows things worked faster/better.....
BUT, there is always a but.....
IT WAS AT THE EXPENSE OF SECURITY.
Compromise the browser (easy to do, CERT, and the Department of Homeland Security both recommend you use a browser other than IE) and you have access to Windows.
Use Mozilla, Firefox, Opera, Netscape, ANYTHING but IE and you will find IE sucks, and suprisingly most of your popup, spyware, and other problems decrease or altogether go away.