That's not too bad an idea ... except that 'flapping' by something not fitting all that tight might do damage ... then again, whatever you put over the shuttle is going to have to be an inch or three thick - thick enough to absorb whatever you want to protect the shuttle from ...
During launch, the CSM is protected by a Boost Protective Cover made from fiberglass and cork. It is jettisoned three or four minutes after liftoff.