Like it or not, for a junior scientist pursuing tenure, at this point in time, journal prestige counts, and at the moment there's very few open journals with close to the prestige of Science/Nature/Cell/NEJM/Lancet/etc. in many fields. If I can get a paper in those, I'm doing it - because my science isn't going to be better served by not getting tenure because I took a principled stand.
It's also offloading the costs. Libraries pay for journal subscriptions. Labs pay for open access publication fees. One is way easier to abstract away than the other, and even in large grants its hard to find the space to pay for multiple papers costing several thousand dollars each. I usually budget for one or two, but hopefully the research output from the project is higher than that.
I think the current model has issues, and there should be a movement in general toward open dissemination of research, but I'm not sure the PLoS model is much better in a lot of ways. Maybe not worse, but maybe not better.
Where this is all headed is anyone's guess. If I had to, eventually most scientific research will just appear in blogs, being treated like personal journals or something, or in research society journals, kind of like what is referenced in the article, basically run by academic research organizations.
My experience with the second model is that there are organizations that would like to run things that way, but run into problems with copyediting, layout and design, and reviewing infrastructure. They kind of think it's something they can just do on the fly but as they do it they realize it's more work. Maybe a company that just provides the tools is the way to go, but at some point that would probably basically become a publisher.
I'm somewhat hopeful about stuff like "arxiv overlay journals". E.g. see description at http://discreteanalysisjournal.com/for-authors
That's a postdoc's laptop. That's several conferences. And it's a single-digit percentage of my startup funding.
It's not insane to not pay that if you don't have to.