There are many modules for Apache, lighttpd, etc. that do this for you.
.htaccess (mod_rewrite used for referrer blocking) is not an option for blocking FLV's, or really any video whatsoever.
It depends on your server setup and configuration which modules can be used, and how hard said modules are to implement.
The most basic and easiest way is if the videos are only to be accessed from your domain(s), and you can make a rule such as "unless the visitor has visited page X in the last 15 minutes, deny all video loads for them".
From there, you can do more complicated things such as have your application link to videos with a secure token in the URL, etc. This would require some form of application modifications however. More and more apps are starting support this.
If you also need to support embeds in random websites, it gets a lot harder to "filter" good traffic from bad. You can setup mod_geoip to do most of what you like most likely, but we have run into some customers who want quite a bit of complex rulesets made - so sometimes it can be difficult.
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