Aha! Dave Hyatt explained the Safari 1.0 font situation the other day. Basically, two major things changed between the betas and 1.0. First, the default font was set to be 16-point Times. This matches the default for Internet Explorer for Windows, which is presumably the browser most sites are tested against. Unfortunately, in my opinion (and I'm not alone), 16-point type looks freaking huge on a small monitor. After setting my default font setting to something sane (in my case, Lucida Grande at 14 points), I found that CSS specified xx-small type (found, for example, in my Shoutbox), became an unreadable pile of poo. The enforcement of a minimum font size (9 points) specified in the prerelease versions of Safari was removed in 1.0 final. The reason for this is revealed in the Dave Hyatt's blog entry -- that many sites use small font size spans as spacers. That sounds like a really unreliable way to position layout elements, but I'm no professional designer.
The Safari dev team threw us a bone, however. Mr. Hyatt mentioned that it was still possible to set a minimum font size via a hidden pref. Hidden pref, your ass is mine.
defaults write com.apple.safari WebKitMinimumFontSize 9
defaults write com.apple.safari WebKitMinimumFixedFontSize 9
(you need to enter those two lines in the Terminal.)
In every non-trivial program there is at least one bug.