There are ways to hide the paths but the technical user will find a work-around.
What exactly are you trying to protect though? If it's a game for instance, you can make it rely on external files that are not visible and even if someone downloads it, it won't run on their website since they won't have the other necessary files.
The best thing to do to secure your flash video or flash games is by not showing them. Have a membership fee for them to see your flash applications if you only want a few to get them. Like what VG said, if the flash apps can play in the client's computer then there is always a way to get it.