Move the FLVs into a non-web accessible directory (or add a .htaccess file blocking it from external access)
Next wrap the FLV output in PHP doing something like:-

<?php
$filename="/path/to/your/file.flv";
$yourdomain = "yourdomain.com";
if (stristr($yourdomain, $_SERVER["HTTP_REFERER"]) || $_SERVER["HTTP_REFERER"]=="")
{
header("Content-type: video/flv");
echo file_get_contents($filename);
}
else
die ("You are not allowed to access this file");
?>

Then point the FLV player SWF at the PHP file instead of the FLV file.

If you want to do pseudo streaming you'll need to use something like xmoov.com (free) but that requires using yamdi (also free) to inject metadata into your FLV files.