Looks like somebody else posted an answer on this thread. IMHO, part of the reason "Master and Commander" didn't do well at the box office was due to poor marketing. Duty, honor, and loyalty are such foreign concepts to Hollyweird that the powers-that-be don't know how to market a film that illustrates those virtues. Guess all that happy powder they shove up their noses has adversely affected their brains.
The reason Master and Commander didn't do well at the boxoffice is because nobody wanted to see it.