For those that don't want to get into the nitty gritty of editing the whitelist someone has come up with a tool. I've made a request to have the tool (it's actually a script) to also make a backup of the file so that it can be easily applied in case of Surface reset.
Windows RT Flash Player Tool brings Flash content to your Surface browser | Windows Phone Central
Windows RT Flash Player Tool brings Flash content to your Surface browser | Windows Phone Central