How was hunley the submarine protected until is recovery?

It wasn't - the Hunley was found to be very well preserved under the silt of Charleston Harbor, fully covered with and full of silt and mud. The visibility at the site was near zero. She had survived 45 tropical storms/hurricanes since her sinking. There was more concern that a tropical storm might hit during the recovery phase.

The biggest obstacle was designing the lifting apparatus and coming up with recovery procedures that would raise the Hunley intact, and at its angle of sinking. This was to preserve and prevent the boat from shifting, which might cause the rivets to pull out, shifting anything inside.