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).