Ok,
I've read enough bs on this one. Let me help you out with the way it really happens.
First off, do yourself a favor and go spend about $150 on a really good hard case. I'm talking the hard aluminum cases. This is to protect your weapon. This is the one I like:
http://www.cabelas.com/cabelas/en/templates/links/link.jsp?cmView=full&type=pod&id=0026824
Next when you go to the airline be sure to declare that you checking a weapon. The clerk will direct you to the proper desk. At this desk they will ask you to open your case. They will look to make sure that the weapon isn't loaded etc. You should take the bolt out of your rifle so their is no question. Do not under any circumstance pack your ammo in the same case. Now the clerk will place a card in the case showing that it has been inspected. Then they will put a sticker on the outside saying that it is a firearm and that it has been inspected. At this point you can request the clerk place your lock on the case. They will do it for you. You will not be able to handle the case from this point until you claim it at your destination.
simple as that. When you get to your destination your rifle will show up and be no worse for wear.