Interesting article in the the Franklin County, Maine Bulldog about compost made at huge commercial facilities. It's not one of those "organic guys are crazy and look how dangerous it is to do stuff without chemicals" articles, but is well-written.
It seems that for commercial composting facilities, size does matter, and smaller is better. At some point, the piles are too large to properly turn, and pathogens like E. Coli, and fecal coliform bacteria are not killed.
What's an organic gardener to do? Make your own! In a backyard pile, you can control what is used: the pathogens mentioned in the article are more likely to occur when animal products like manure are used. You can also monitor the pile to ensure it heats up properly even if you do use manures.