In the old days, before 3.0, Safari had an annoying habit. If you pressed Cmd-Q with many windows and tabs open, then Safari would quit. This could be incredibly frustrating; especially when you accidentally pressed Q instead of W.
Safari 3.0 fixes it properly. Apple has included the option of prompting the user on close if multiple tabs or windows are open.
However, if Taboo is still installed, you cannot close top level windows.
Taboo lives in one of the following two directories.
~/Library/Application Support/SIMBL/Plugins/Library/Application Support/SIMBL/Plugins
Remove it, and Safari 3.0 will work as intended.