Problem is the nofollow attribute only ever meant that page rank should not flow. Many people thought it was also an instruction to Google not to follow the link. They have always followed any links they find regardless.
For quite a while now PageRank has not been the only scoring system of a web page/site so seeing a lot of nofollow links to a target could still be used in helping with its final position.
The one good thing about the nofollow attribute was it proves to Google that you're not attempting to manipulate SERPS.
For me personally, I have been watching this new setting and trying to understand quite how they will treat them. I can't believe it will make much difference in terms of ranking but who knows. The Jury is still out on that one.
Knowing a site gets most of its links from user-generated content or from adverts is interesting but should that really affect SERPS ? Maybe, but up until now, Google had no clear way of knowing so I would think its still going to be a while to be able to answer how this will play out. Many sites are still just using nofollow so until that changes drastically it will be hard to get any meaningful tests done.