Switch to Safari and choose Safari -> Reset Safari... and Reset. Switch back to the Terminal and cat Cookies.plist again. Surprise, surprise they're still there. Now, switch back to Safari and open Preferences -> Security -> Show Cookies. The list is empty. Back in the Terminal, cat Cookies.plist will also show that the list is empty.
[robg adds: This does seem to be a bit of a bug -- I even tried quitting Safari after choosing reset, but the cookies file was still full when I checked it after re-launch. Very strange...]

