I just suck it up and pay. While I may not agree with the charges, it's not like it's a hidden fee. I'd rather know that my rather expensive bike has the protection of a hard case. We use a Velo Safe.
You could add S&S couplers to your bike, then it would fit in an airline legal case. But you'd probably need to take 10 trips with your bike to make it cost effective.
V.