I had the same problem with Midori & Webkit from the Webkit Team's PPA on a minimal installation of Ubuntu. But on my desktop machine with Ubuntu 8.10 flash did work in Midori.
But after running
(even when it's useless when you only have flashplugin-nonfree) and
sudo update-alternatives --config mozilla-flashplugin
it somehow worked. Seems that under some conditions Midori doesn't get the correct location of libflashplayer.so in Ubuntu 8.10.
export MOZ_PLUGIN_PATH="/usr/lib/flashplugin-nonfree" && midori