Check the console, and look for a line like:
WebProcess(738) deny file-read-data /Users/ats/FontExplorer X/Font Library/M/Minion Pro/MinionPro-Regular.otf
When I saw this problem, it's because the sandboxing in Lion does not allow safari to read the font file. I have a bug report open for it, I suggest you open one as well. My fonts are in that location since I have Font Explorer X Pro manage my fonts, and it autoactivates things, but unfortunately the sandbox doesn't currently allow that to work.
Solution right now is to move your fonts to the usual system location. Or, potentially, to change the base application entitlements to allow the directory they're in, but since the file is clearly marked "Do not change, not user editable, autogenerated, private api, etc" I don't want to discuss that until I've verified that it works.
