Nature is paid to do two jobs.
1, Provide a copy of the paper on paper to sit in a library for 100s of years.
2, Certify that a paper has at least been written by somebody vaguely reputable and has been peer reviewed
Originally the first job was the main role, now with the internet the second is far more important. I am happy for my institution to pay for a paper copy of Nature in order that there is a universally recognised 'I am not a crank' stamp to put on my work. Think of it as an SSL-cert for my pages.
Yes I would like there to be a free open online web-of-trust for peer reviewed papers - but for now I have no objection to Nature doing that.
And I would much rather have a commercial publisher do it than have it mixed in with a professional body like IEEE/ACM/IOP who have a whole other set of agendas.
It could be that the conflict here is with our rather strange notion of intellectual property and a free market economy. Robert Laughlin's The Crime of Reason: And the Closing of the Scientific Mind makes the case that the two are antithetical. A free market requires that something be secret and not generally available to create an artificial shortage and pump the price.
Perhaps we need to rethink what constitutes intellectual property. What sort of an intellectual property policy would you propose to your university? Who should own ideas? Or should they be held in common? Will Mickey Mouse ever slip into the public domain?