You may need to add it to the panel's whitelist for it to show.
dconf-editor is an application that allows you to access and change these configurations so:
Once installed run: dconf-editor
sudo apt-get install dconf-tools
Once open navigate to:
desktop > unity > panel
Then edit the Value for systray-whitelist to add skype. I think it needs a capital S so add 'Skype' after a comma at the end of the current value string.
Close dconf-editor, logout and back in and hopefully a Skype icon will go to the notification area when you hit that close button.