FWIW, while Cell and Nature are both owned by private companies, Science is run by a non-profit (the American Association for the Advancement of Science), and articles in science are made freely available two years after publication.
Having read his manifesto, I don't think his issue with with corporate publishers per se. His issue is with the culture of judging the quality of work by the prestige of the journal it was published in. That allows journals to further exploit the process; they have a large incentive to publish flashy research rather than quality research, because flashy research gets more citations -- thus making the journal more prestigious.
While I agree this is a flawed system, I'm not convinced that open-access journals are the solution; there are already more prestigious open access journals -- like Physical Review X and the New Journal of Physics (both of which are run by non-profits with prestigious, closed-access journals).
To some extent, you need both flash and quality research. I'm sure someone could do quality research on the physics of navel lint trapping, but pretty much no one would care; the research isn't interesting, and it wouldn't be worth the effort to peer review. So, for better or worse, I don't think the flashy factor will or should totally go away, although I agree it should be reduced.
That said, I am a fan of open-access journals, but I need something to publish first. I guess I should get back to research and stop wasting time with Slashdot posts....