By the way, since PLoS is a non-profit, do they publish their cost structure anywhere? Is it possible to say where the money from a publication goes, for instance?
Unfortunately, it doesn't break down the operating expenses of $12.21M (2010) with any more granularity than $6.68M on direct publishing expenses, $5.465M on operational expenses and $65K on advertising & marketing.
I heard back from the PLoS people. (Aside: they are WAY more helpful to random inquiries than any of the for-profit publishers). The best information on this can be found in their tax returns, which are available at http://www.plos.org/about/what-is-plos/progress-updates/
