The sheer number of original sources and secondhand sources that each need to be individually vetted clearly requires a lot more work and skill than using a well-curated package manager.
And a lot of vendors that should have been trustworthy ended up taking advantage of it by sneaking unwanted software in with the good stuff. Off the top of my head, Adobe did this. There was a glorious time in the 90s and early oughts where seemingly everything was trying so install another toolbar into IE...
There aren't any well curated package managers for normal users.
Linux distributions like Debian barely make the cut for technical users, folks who are used to going to forums and finding alternative packages. Even so, Linux packaging is filled with drama, contradictory standards, alternate sources required for specialized applications, and occasionally downright bad decisions (like shipping insecure CAs). The only way to scale such a model to normal users is the way Apple and Google have done it on their mobile platforms, and frankly, those stores still have a fair amount of malware in them (Android especially - it's sandboxing that is actually useful here, not a package manager) and come with pretty massive anti-competitive downsides.
And some users liked the toolbars. Just like some users like Facebook. Toolbars aren't actually the problem - it's the way they slurp up your data - it's not a problem that needs a technical solution, more of a user education solution (just like Facebook).
I didn't say that package managers are perfect. I think they are a lot better. They have downsides related to centralized control and contradictory interests, but I believe the good outweighs the bad and you can usually install software from somewhere else if you really need to, with one conspicuous exception.
Most Linux distributions fit for desktop use ship with an "app store" presentation so I think accessibility has been addressed.
And a lot of vendors that should have been trustworthy ended up taking advantage of it by sneaking unwanted software in with the good stuff. Off the top of my head, Adobe did this. There was a glorious time in the 90s and early oughts where seemingly everything was trying so install another toolbar into IE...
There is plenty here to be critical of.