I'm not as convinced this is terribly skewed away from the normal. Outside the Bay Area, the large organizations that hire thousands of programmers primarily use Windows for development. For example, go to any Defense Contractor (Lockheed, Northrop, etc) in the country and sample the computers they use for dev work. Each developer probably has a Windows box they do everything on. There might be some Linux boxes mixed in, but those will probably be headless. Or the developer runs Linux in a VM on top of Windows.
While in the Bay Area, we might think these are skewed because everywhere we go we see Mac laptops, in reality, the employees at big corporations are going to outnumber us.
I suspect that the survey is skewed in other directions when it comes to large corporations, though. I would expect to see much more Perforce if the big not-primarily-computer-companies were included, because for many years Perforce was pretty much the only game in town for large, multi-million-line codebases. I still can't imagine Lockheed running their sourcebase off Subversion or VSS; even when I interned at a mid-sized (~100 person) government contractor, we used Perforce.
I think the survey is representative of the geographically-distributed, Joel-on-Software reading, micro-ISV crowd, and not much else. Micro-ISVs often develop on Windows (because that's what their founders are used to) and use Subversion (because it's fairly easy to setup and generally adequate for 1-10 devs). I suspect you'd get very different numbers at YCombinator or Google or Lockheed, though.
Another mega-corp data point: 15,000 Engineers plus everyone else uses desktop/laptop windows XP. Linux is used on the supercomputing clusters and on test equipment in the factory. IT controls the desktop domains, while the engineers control the clusters and test equipment.
I can confirm this (working at mega-corp) and can also add that a lot of specialized and embedded tools are primarily hosted on Windows. Even high-end CAD and modelling tools are primarily on Windows where I've worked.
High-end CAD tools used to be run almost entirely on Unix systems (Solaris, SGI, HP/UX, etc.). Back in the 1990s Windows systems couldn't handle these tools the way Unix workstations could, but once that changed there was no reason to spend far more money on a workstation. Perhaps if Linux had become popular a few years sooner the transition in high-end CAD would've been from proprietary Unix to Linux. See for instance http://www.ptc.com/partners/hardware/current/support.htm where support for various *nix are being phased out by Parametric Technology, Linux included.
Yeah, I remember those days well, we had Unix boxes for CAD and 386s with Win3 for office work side-by-side. I think you're right - the transition to Linux would have been an obvious choice if the timing had been better.
While in the Bay Area, we might think these are skewed because everywhere we go we see Mac laptops, in reality, the employees at big corporations are going to outnumber us.