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.
As much as I liked Perl back in the day, it did sometimes earn its reputation as a write-only language!
At my company they really locked in the project being dead if the original contributors left.
Perl propped up regex (JavaScript regex is based off of it), so I get the impression Perl practitioners tried to make all the code regex-y as possible as a cultural thing.
And this became a joke and meme.