His mission failed with The One Ring taken from him, and tortured by the cruel servents of Sauron, Frodo faces a world in which all he has loved will be lost. From the darkest chambers of Mordor there appears no hope for salvation.
Much the way saints have been portrayed in religous works of art, the nudity Frodo emphasizes his vulnerability and desire to be spiritually released from the pain of the mortal world. This is not the isolated act of a single orc beating down a frail Hobbit, but rather represents the oppressive nature of the will of Sauron threating to place all of Middle-earth beneath his rule. Shadow and shackles are the destined future for the inhabitants of Middle-earth.
Something was lying on the floor by the wall under the window, but over it a black orc-shape was straddled.
It raised a whip a second time, but the blow never fell.
- The Tower of Cirith Ungol, The Return of the King, J.R.R. Toklien
A detailed blog post on the color structure of this work was posted as The Mud of Frodo on the Muddy Colors blog.