Apple Font Book app allows users to “disable” fonts, but in reality the font is left in one of OS X’s font’s folder, and flagged to not show. I’ve always considered this a poorly constructed feature, because technically the font is still active, it’s just being ignored. Because of this, I strongly recommend not using Font Book.

If you suspect that a user has previously disabled fonts in Font Book, and you want to get things back to a virgin state (all fonts in a legit font folder are active), perform these steps.

OS X 10.6-10.8
1. Move to Trash ~/Library/Preferences/com.apple.FontBook.plist
2. Move to Trash if found ~/Library/Preferences/com.apple.FontRegistery.user.plist
3. Open Terminal and enter this command: atsutil databases -removeUser
4. Reboot the Mac, then empty the Trash

OS X 10.9 Preform the same 4 steps as with OS X 10.6-10.8, but before rebooting…
3b. Use the app EasyFind to search the entire drive & locate the hidden file named app.com.apple.FontBook.playlist, reveal this in the Finder, then move to Trash