Dave,
We always put ours in a rolling waterproof Pelican hard case with a handgun. When you declare your firearm they only search it once, in your presence, and then ask you to lock it back up and it stays that way. Then if some TSA nerd wants to get fingerprints all over them they have to do it in front of you. They also don't tend to 'loose' luggage that contains a weapon, it comes out at the special luggage desk. Keep a close eye though, we've had it pop out on the regular belt as well once.
-HD