mod_php was dramatically simpler to use than mod_perl. If the sysadmin set it up, you didn't need to know it was there, and your regular PHP just ran really fast. That and nothing else really copied the "scriptable HTML file" paradigm which some people really really liked and made a very low barrier to entry compared to Perl. That's really what kicked off the demise of Perl -- it stopped being the most accessible way onto the internet. PHP also didn't screw up their major language upgrades like Perl did.
RoR helped Ruby push off its inevitable demise for a while, but it's going the same way as Perl. Python got lucky that it's become the defacto choice for everything ML.