I had higher hopes for the original article in discussing specific technical reasons for choose one API over the other aside from the issue of platform support.
From my perspective, the the controversy boils down to a handful of actual issues:
* Quality of drivers. D3D drivers have historically been more solid than OpenGL drivers on Windows. This is less of an issue these days with Nvidia. Unfortunately ATI OpenGL drivers remain a bit flaky.
* Market. I believe that the very high end graphics workstation market (think Hollywood CGI artists, CAD, etc) is still invested heavily Unix (Linux) based tools. Nvidia has a much bigger foothold in this market than ATI which explains why Nvidia has superior X.org drivers and better OpenGL support all around.
* Bleeding edge technical features, if you are trying to achieve some advantage in rendering quality over your competitors. This makes sense in the graphical arms race of gaming, but most of the rest of the visual simulation industry (3D modeling, CAD, scientific computing, government/military, etc) don't care about the cutting edge as much.
* What your 3D engine of choice supports. Writing a whole 3D engine from scratch is going to be silly most of the time with the many commercial and open source 3D engines now available, so you are not going to be writing a whole lot of bare D3D or OpenGL code.
Like a lot of other areas, Microsoft's development solutions work great if you stay in the Microsoft ecosystem. As a pure business decision sometimes it makes sense.
What irks people (including me) is when Microsoft deliberately or de factor freezes out the competition; this is where we end up with frustrating situations like the case of ATI having inferior support for OpenGL on Windows. There's no technical reason for it, just someone manager's decision on how to allocate developer resources. Longtime Linux users know this is a story that has played out with many devices; usually there is no technical reason a piece of hardware can't be used on Linux, it is simply a matter of the manufacture choosing whether or not to devote additional resources to supporting platforms other than the one with the biggest market share.
So ultimately it is about mindshare and putting pressure on Nvidia and ATI step up to the plate to have good OpenGL support, and encourage Microsoft it is not in their best interests to screw over Windows OpenGL users.
(did I mention enough times how much ATI OpenGL driver quirks annoy me?)