My take is a lot of that Web 1.0 stuff was total spaghetti code, hardcoded to a table layout, full of injection holes, etc etc. (It was like everyone did my first CGI script x 100.) So in that sense Perl wasn't any different than classic ASP or cold fusion or etc, it became associated with bad legacy code. And because there was no 'Perl 6', people had to choose something else.

(There's stuff about the perl language, but that's probably secondary.)