One of the reasons is because during all the time when IE was essentially the only browser (after first browser war in 90s and prior to mid-2000s) Microsoft implemented standard in a way they wanted, regardless of how features were supposed to work according to said standards. Thus, IE often doesn't follow, say, CSS specification, and web designers have to implement special workarounds to make things work as intended.
Also it was really slow, unsecured and unstable. I don't know if IE became better nowadays (I have never actually used it anyway).
