I have Specialized Stumpjumper Evo FSR and as all the FSR frames its' shock is underneath the top tube. Now the issue that the only option to put the bike on the rack is to put the shock shaft on the rubber U that's on the rack. The question is, can I do something to ensure avoiding scratching shock shaft? Or the only way is to get a new rack?
You can purchase a rack adapter thats primary use is for mixte, womens bikes or bike with angled top tubes. It is a removeable bar that attaches to the seatpost on one end and then attaches between the stem and the headset top bearing at the other end. You then hang the bike on the rack by the adapter.
You definitely should not be mounting your bike on the rack by the shock- that's just asking for trouble. The adapter that mikes suggested should do the trick for you, but if you want to use this as a reason to get a new bike rack I would suggest you look into a Thule T2 or Yakima's equivalent. I owned a handful of tray mount style hitch racks that were relatively inexpensive before finally purchasing a T2. Now that I've owned it for a while I wish I had have sprung for it in the first place. Incredibly easy to use, very secure, and virtually no restrictions on the type of bike it will accept. Completely worth the extra money.