I installed Ubuntu via Wubi on Windows 7, and I upgraded my laptop to Windows 8. The dual boot option and Ubuntu work fine, but I cannot uninstall it; it does not appear in the programs.
You can refer to this WubiGuide for uninstallation.
When you upgraded Windows it replaced the registry entries so it can no longer uninstall automatically, but the Wubi Guide shows how to uninstall manually. This also shows how to manually remove the boot entry from the Windows Boot Manager