OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). So hold the Shift key until you get to the desktop. It just takes longer to get to the desktop in Safe Mode. Whether it's a Safe Mode boot or a normal one, you get the same progress bar. You can let go of the Shift key at that point. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Or at least, 99% of the time, that's what's wrong when the fonts are listed in Font Book, but none, or only some of them appear in your apps.
What's wrong is Font Book's database is corrupt. All of your fonts are still on the drive. FontNuke doesn't delete fonts, it deletes font cache data.
