From the article, it weren't independent sources which were punished, but far-left and far-right sources.
> However, in addition to AlterNet and other left-wing news sites, Rosenfeld said right-wing, alternative media outlets have also seen a reduction in viewership due to the change in Google’s algorithm.
So? Independent news sources almost always have a non-mainstream political bent; that's why the writers aren't just writing in the New York Times. I don't think most people understand "weeding out fake news" to mean "only allowing a narrow spectrum of respectable opinion." And these sources do real reporting and break real news.
