Webdriver is specifically automating only the browser, not any of the plugins that run in it like Flash or JavaApplets.
Flash does have an automation API, it is possible to add JavaScript hooks to open up access to the JavaScript external interface. You can then implement the Webdriver interface as a bunch of external interface calls that translate the calls into Adobe Flex automation calls. Then you could treat the Flash application as if it was an IFrame.
I've done a simplified version of this before for another employer (proprietary framework). I know this is very possible, but I don't know if anyone else has done it yet or open sourced it.