There's a lot of stupidity here (or perhaps one might charitably call it excessive glee, or even plain old clickbait), but it's been a long time since 95% of computers ran Windows, if that was ever true in the first place.
You'd have to start by defining "computer". If we use a technically reasonable but broad in journalism's terms definition of "device containing a CPU with integrated MMU", then we're including every mainframe, server, desktop, laptop, smartphone, tablet, industrial control system, laser printer or multi-function document management system, router, network or storage switch, storage system controller, sound mixer, and countless other devices. A very small and diminishing fraction of those machines run Windows.
Even if you limited the definition to include only things we traditionally think of as computers, namely mainframes, servers, desktops, and laptops, Microsoft's market share is something like 30%, though it's very difficult to measure and once again subject to definition; see https://en.wikipedia.org/wiki/Usage_share_of_operating_syste.... And again, that's been declining for a long time. Even the most generous interpretations that include only desktops and laptops don't get you to 95%; you can narrow-definition your way up to about 90%, and that assumes "market share" includes copies that were made in violation of license and/or law (and thus for which Microsoft received no money).
The reality is that Microsoft is a niche player, not because they lost a market they were previously winning but because that market itself became a small part of something much bigger, in which Microsoft was never especially competitive. As noted by the author, they've been investing heavily in changing that, but the early returns aren't much to talk about. Windows Mobile/Phone is a complete dud, Surface is a weak seller despite recent improvements, and Azure is at best a very distant second in IAAS (see http://www.datacenterknowledge.com/archives/2015/05/28/gartn...). What's remarkable is not that Microsoft is doing so poorly but that they're the only enterprise computing company that even appears to be trying. I think that's what the author was expressing. The characterization as "fucked" comes from Ashlee Vance and should be given the credibility one would assume considering the source. There's little question that most of these companies' positions of relative importance are in decline and have been for a long time. But some, especially Microsoft, still have enormous sums of cash and businesses that are continuing to generate more of it. However irrelevant such a company is, it's still a long way from going out of business. Conversely, no amount of cash is a substitute for organic sales growth.