Ship with a protective inner layer (5)
I believe the answer is:
liner
'ship' is the definition.
(liner is a kind of ship)
I cannot understand how the remainder of the clue works.
(Other definitions for liner that I've seen before include "Cosmetic; fine paintbrush" , "Large passenger or cargo ship travelling on regular route" , "It covers bin's interior" , "Removable inner skin or large passenger ship" , "QE2, perhaps" .)