I'm not really seeing the comparasin. The main plot of Master and Commander (the movie anyway; haven't read any of the books) is capturing the enemy ship, while its side plot is about the captain's pride. The main plot of VotDT is an adventure story seeking out lands and the end of the world, while its side plot is the redemption of Eustace.
Maybe visually they could be similar, but really I can't see that happening either. Sorry, I don't really see any connection between the two except for they both have a ship and they go to the far side of the world (however for different reasons).