Just flew on Alaska from Seattle to Hawaii last month with my bike packed in a SCI-Con travel case (07 Specialized S-Works). I have flown my bike several times before in this case with excellent results as you only remove the wheels and secure the bike by the dropouts to the metal frame in the bottom of the case. Alaska waived the fee as a frequent flyer courtesy so I was good to go for a week of riding. Under new guidelines the TSA removed the bike from the case for inspection and didn't bother to reattach it to the metal frame, allowing the chain stays to bounce against the case frame the entire trip - chipping off the outer layers of carbon and cracking through the chain stays, leaving me without a bike to ride upon my arrival.

Because the TSA had opened the bag and stamped the claim tag, Alaska wouldn't accept a damage claim and left me with the only option of filing a claim with the TSA for a replacement frame. They'll let me know the results of their investigation within 6 months.

Moral of the story - don't fly your bike, ship it UPS with full insurance.