I think the most important point was brushed over in the article--that journals offer prestige. Scientists are entirely aware of the problems, yet they still volunteer to submit their work to them, because they significantly improve the chances of promotion and tenure. These things are already tremendously competitive, so most would rather not volunteer for a handicap by publishing in other venues.
A big part of success in modern scientific research is ability to secure funding, so if you put your thumbs on the scales enough, it could catalyze a move to open access journals as the "prestigious journals."