(Via Open Access News.)
Odd though, for a journal that is only ever (as far as I know) intended to be published online, to offer the articles using PDF rather than HTML. Doing so prevents any use of lightweight 'semantic' markup within the articles, such as microformats, and tends to make re-use of the content less easy.
Doesn't seem so hard to figure out. HTML is awful for mathematics and scientific graphics. Just compare our recent paper in HTML and in PDF, even though the math in the PDF version is not as readable in PLoS's required Word format as it was in our original LaTex.