One thing I discovered in an attempt to follow up on this Down to Earth post is, the government doesn't seem to do a good job of tracking deaths due to food poisoning. This site has some interesting figures. I'm not quite sure what the difference between roughly 40 deaths per year reported and the 1000 deaths per year estimated tells us about the safety of the system.
I'd throw out this logic, which may be wrong. The stuff that gets reported to CDC is the widespread pattern of illness, which might result from salmonella somewhere in a big mover in the food chain; the stuff that doesn't get reported is salmonella from the smaller movers.
Looked at another way, if there's one thousand deaths in the food system and 40,000 deaths in the transportation system each year, and we eat more often than we drive, food is very, very safe.