Windows was great in that it allowed multiple hardware vendors to compete on hardware without having to also design their own OS. It was great in that it allowed multiple corporations to market the same platform. And as it grew, it was great in that it allowed developers to write an app once that ran nearly anywhere.
There's a lot more to "great", as applicable to an operating system, than even usability, stability, graphic design. A lot of times the things you value, as a developer, aren't what the general public does. You might want an OS that's very much like Linux but with a much better GUI. Most people just want their PC to cost $300 and run any program they buy or have bought in the past.
So Microsoft's OS was clearly great by far more people's definition of the word than Apple's, and it reaped the rewards.