Considering the overwhelming majority of mainstream business software runs on Windows PC's and Windows Server environments, I'm not so sure Microsoft is running scared.
What they ARE doing is giving developers a choice in the environment they want to develop without consideration to the underlying OS. Personally I think it's a good thing. It's going to expand capabilities beyond the individual OS platforms themselves.
Well, yeah, I overstated it a bit. But they're nowhere as confident in their ability to execute as they once were, and their recent forays into mobile products and cloud offerings haven't been stellar successes. Azure is credible but nothing like Amazon, etc. And the mobile side is dead -- Ballmer's famous laughter at the iPhone is pretty hollow these days.
They rested on their laurels, relying on their monopoly status, for long enough that their competition had time to grow from negligible to credible to substantial. MS still has the majority, but it's the trend that they are rightly worried about.