I cannot find 2011 data, but over 2010 their net surplus was $2.8M, $2M from donations and $0.8M from operations (http://www.plos.org/media/downloads/2011/Form990_2010.pdf)

I use 'surplus', not 'profit' because PLoS is a non-profit. They can build up reserves to guarantee continued existence in times of hardness, or for future growth (for example, they may need money in the bank to rent or buy offices, or to make them more attractive to prospective employees (who is going to work for a non-profit that, every month, hopes to be able to pay your salary?)