Ok, so of 2 billion desktops (estimated 2015), that's 40 million Linux users. Of that number, the cross section between "Linux Users" and "readers of Neal Stephenson's works" are probably quite high. It doesn't take much to be faced with a "horde" as any person popular among a niche crowd can easily attest to.
Not to mention at that time Linux was gaining a lot of share in the service space replacing legacy UNIX, Novell and even Windows NT. Just because "hordes" weren't using it on the desktop doesn't mean there weren't hordes who were aware of it and used it at least sometimes, if not daily.
In 1999 I worked for a company in Canada that replaced servers that supported their products and internal servers that ran SCO UNIX with Red Hat boxes. Saved them a lot and we managed to keep everything working as it had on the old servers.
I didn't think of myself has part of a horde at the time but I sure was opinionated about Linux and could see myself being one of those "know-it-all-kids" that hassled Steve had I read his stuff at the time.