Not just PLoS...look at JBC or other journals and you'll see the little disclaimer that the pages are marked as advertisements because of the way the printing costs are defrayed. Also, it already costs the author money to submit a paper for publication to defray the costs of editing and peer review. Peer review costs nothing, it's the shipping to the reviewers and admin costs.
Publishing on the web is not a good alternative.
Sure it is. It's already happening. These days, results are increasingly multimedia. On top of that, journals want high levels of stringency on their papers, but they don't have room to show all results. That's why they invented supplemental results online. Libraries have to adapt and subscribe to more online journals. Sure, you do go out and dig up the 60 year old paper on occasion, but digital distribution won't do away with it. That's silly. And to answer your "profitability" statement, have you noticed that the bulk of scientific journals is actually advertising? It's like Playboy, the good stuff is only a small fraction of the magazine... yeah, that includes the articles we all read in that fine publication.
Also, don't forget how long people have been pushing for this free access. Harold Varmus, the former NIH head, has been quite vocal about this matter for some time now.