Why did that happen? In my opinion, PHP had two major advantages over Perl:
1. mod_php for Apache could safely be run in a shared hosting environment, so hosting for PHP was cheap and ubiquitous. mod_perl couldn’t be run in shared hosting, so anyone doing web development in Perl was stuck with either using CGI, or paying for more expensive dedicated hosting.
2. PHP’s approach made it easier to get started for people who were new to web development, or new to programming entirely. This was important in the late 90s and early 2000s as a huge number of people started doing web development for the first time.
By 2000, PHP was already the dominant “scripting language for the web”. If the Perl community had focused on improving web development, then maybe Perl could have caught up, but they focused on Perl 6 instead, and PHP continued its growth without much serious competition from Perl for web development mindshare. MediaWiki was written in PHP in 2002, and both Facebook and Wordpress were written in PHP in 2003.
The article focuses on Python, but during the relevant time period (roughly 1995-2005) Python was a niche and unorthodox choice for web development. Python finally started to gain traction for web dev in 2005 (Django, Pylons, TurboGears, and web.py were all released that year), but by that point Python was mostly competing with PHP, and Perl was already much less relevant.
In summary - the article focuses on how Perl lost the market for scripting, but scripting was always a smaller and less important market than web development, and PHP killed Perl in the web development market. If Perl had stayed relevant for web development, it likely would have stayed relevant in scripting as well, because programmers like to use languages they already know (see: JavaScript). Perl 6 was the nail in the coffin that ensured Perl wouldn’t catch up in the web dev race that it was already losing.