That's not true. Linux was very popular in 1998-2000 already, with RedHat and SuSE distros everywhere. Server software was usually written with CGI api, in C, Perl or PHP. Also Windows NT 4 and 2000 servers with ASP (classic) with web server software written in VBScript or JavaScript (yes, ASP classic had JavaScript/JScript support on server). Well known top websites of dotCom era like EBay and MySpace run on Windows servers back then. Back then Windows was a lot more popular on servers than nowadays. Also old school UNIX wasn't such a popular choice - name me five well known dotCom era startups that run on UNIX (in 1998 to 2001) instead of Linux or Windows.
@downvoter: care to explain?