Found an interesting (but biased) article about salmonella within eggs. Apparently there's a 1-in-20,000 chance that a chicken will carry the bacteria in its reproductive system. The eggs end up getting infected with just a few bacteria before the shell forms.
http://news.discovery.com/human/health/egg-salmonella-bacteria.htm
I wonder if the confined-feeding is the issue or if it's just a low-probability event that you probably won't see if you keep 6 hens.
Anyhow, it's nice to have open-minded discussion on the topic rather than fear and criticism that I've experienced in the past.