> my impression was that by the 21st century, Linux was becoming dominant.
This is just bias and rewriting history. Linux was popular among younger admins and developers. It was a verve among that generation. Many were running it by 1996, and any who did will have the false impression that it was dominant because they were exposed to it. And while Linux was in the datacenter by 2001, it was not used for web front ends, it was for running backend processing. What I am saying is that Linux had not been widely adopted by the corporate or industrial space as webservers by 2006.
If there were any public facing Linux webservers in 2006, they were in such a minority that claiming it was becoming dominant is only said with the benefit of hindsight, because by 2012, Linux did take over most webservers. But in 2006 no one could know that, because most webservers, 80% or more, from 1994 to 2006 ran NetBSD, and IIS never had as much deployment as NetBSD webservers.
Again, I am not talking about any MAMAA. I am talking about Joe's Electronic Shop, and Xie's Ceramic Hippos, and the vast majority of all the public facing webservers online in the 1990's were running NetBSD, because by the mid-90's, it became ordinary convention, thus no one said, "we should document this for historical purposes."
The UNIX Wars were over and BSD won, so there was no hemming and hawing about what OS to use for a webserver. It was a choice between a handful of proprietary pay OS (Windows Server, AIX, HP/UX, etc.) and the free BSDs. For whatever reason (stability, maturity, practicality, etc. etc.), NetBSD was the vastly more popular choice for webservers, right up until the Linux verve came in and fixed something that wasn't broken. Linux was just a preference at best and a fad at worst. It brought no new features (Apache 2 is Apache 2), was not more secure, though it booted faster, NetBSD never need be rebooted. Linux took over like Pepsi took Coke's marketshare, and there was no rational reason behind this. Today, one is as good or bad as the other. In 2006, Linux was not mature. I know this because IBM scrapped their wide-deployment Linux plans in favor of continuing to develop AIX, which as awful as it is, it was far more stable and mature than Linux in 2006.
Linux only got great, like, astoundingly great (which means as good as any BSD or SysV variant), maybe a decade after the Millennium. In 2001, no company, not even the small ones, were trusting Linux for public facing anything. Maybe Linux had small gains in the web space by 2006, but it couldn't have been more than a few percent, if even a fraction of a percent, of the web. In 2006, the web was nearly entirely Windows Server IIS and NetBSD Apache 2, with the rest in small minority sharing a few percent, Solaris, AIX, HP/UX. And Mary's Coffee Mugs Boutique was not running AIX or Solaris, would have cost a fortune. NetBSD was convention for webservers, and it was free, very well-documented, well-supported, had dozens of thousands of free ports available through pkgsrc, and was very stable, and a mature OS. So it should not be surprising in the least, because it worked, and Linux was not ready, and it wasn't ready because, though the younger IT gen was ravenous for it and crusading for it, the grey beards in decision-making positions hated it (I think because Linux arbitrarily messes with the established directory structure of UNIX, so things were not where they were expected to be, causing frustration among the most experienced UNIX & BSD admins).
I would bet, before Craigslist migrated to CentOS sometime after 2004, from inception and for the entirety of the 90's and the early naughts at least, it probably ran Apache on NetBSD. How the heck can anyone find anything about what OS Newmark was running except the man himself? (I'm fishing to see if Craig lurks here, but at 69, I hope he's lurking on a yacht somewhere instead). I'd also be willing to bet that Amazon was originally hosted and launched from NetBSD servers, but I'd also bet Jeff doesn't remember.