I don't recall any reports on FT of TSA pawing through laptop contents, but there have been reported cases of mileage runs where the airline turned an innocent passenger over to federal and local law enforcement who then pawed through the victim's laptop's contents:

http://www.flyertalk.com/forum/showthread.php?t=634740

If you are serious about protecting your privacy, encrypt your files and be prepared to refuse to turn over the password.