"How is that an indication of quality?"
To be fair, same could be said about press releases, article marketing, forum signatures, profile signatures, guest posting, link exchanges, link requests, broken link requests, link bait, comment spam, forum spam, sploging, paid links, etc etc.
Link building is all about artificially inflating quality signals and not about building actual quality signals. Just because there's a sliding scale of spam involved with each technique, doesn't change what is.
Personally, I think directories are a grossly underrated potential revenue stream for website owners. A combination of SEO spam and Adsense induced laziness probably makes them less appealing, but if you can design, build and cultivate a good directory, it can really be a good little earner.
From a search point of view, such a directory should tecnically pass some kind of qualitative signal, but that's only in theory. In practice, there are only a handful of directories like that, compared to thousands that have grown from the DMOZ-clone / link spam era. It makes sense that Google would take a swing a directories in general (although I'd add again, I've not seen any impact on some of the better directories).
I just hope it serves as an incentive to some people to reassess their strategy with directories and help build better ones, rather than just let the concept die a victim of Google spammers.