My recent research has led me to the conclusion that hotlink protection for Flash video files is quite difficult as Flash video players do not send referrer information when they access the video. If I'm not mistaken, .htaccess depends on this referring information to determine whether or not the video is being hotlinked.
Your best option, given the above information is accurate, is to seek out and implement some streaming video solution as they normally afford you hotlinking protection.
Outside of this, you will probably want to obfuscate the link to your videos (such as using
www.domain.com/stream.php?video_id=X as the URL for the video) and/or implement some solution where the names of your video files are changed at certain invervals.
Hopefully someone more knowledgeable than myself will chime in.