1. It pulled away folks who would otherwise have spent time improving Perl 5 (either the core or via modules).
2. It discouraged significant changes to the Perl 5 language, since many people figured that it wasn't worth it with Perl 6 just around the corner.
3. It confused CTO/VP Eng types, some of whom thought that they shouldn't invest in Perl 5, since Perl 6 was coming soon. I've heard multiple people in the Perl community discuss hearing this directly from execs.
Of course, hindsight is 20/20 and all that.
Also, even if Perl 6 had never happened the way it did and instead we'd just had smaller evolutions of the language in major versions, I think usage would still have shrunk over time.
A lot of people just dislike Perl's weird syntax and behavior. Many of those people were in a position to teach undergrads, and they chose to use Python and Java.
And other languages have improved a lot or been created in the past 20+ years. Java has gotten way better, as has Python. JavaScript went from "terribly browser-only language" to "much less terrible run anywhere language" with a huge ecosystem. And Go came along and provided an aggressively mediocre but very usable strongly typed language with super-fast builds and easy deploys.
Edit: Also PHP was a huge factor in displacing Perl for the quick and dirty web app on hosted services. It was super easy to deploy and ran way faster than Perl without mod_perl. Using mod_perl generally wasn't possible on shared hosting, which was very common back in the days before everyone got their own VM.
All of those things would still have eaten some of Perl's lunch.
I started programming in the late 90s using Perl as my first "real" language. When I first saw some Python code (2.3 if memory serves), I found it much easier to understand. Not necessarily easier to write, but diving into a Python codebase 6 months later was a lot easier than doing the same than with Perl. Purely subjective, but I was far from the only one, even if quite a few people at the time preferred Perl.
Later, when the Web really took off, running PHP 4 was much easier to get going than either Python or Perl, so a lot of us went with that.
And yeah afterwards JS with node.js in particular. The millions pumped into it by Google certainly helped.
There was also a time a bit later with Ruby getting really popular. Not just for new projects, I heard of some codebases migrating from Perl to Ruby, when the writing was on the wall for Perl 5.
Go, I think when it became popular not many people were still using Perl. Also not really something you would use to bang out a quick script with. Probably more of a competitor to Java.
As for me, back to Python as my bread and butter. Probably haven't touched Perl in 20 years at this point. Looks like gibberish to me now...