Edit Mixed up real and fake ship names.

Hey OP, I'm assuming you're asking about the movie Master and Commander: The Far Side of the World. The book Master and Commander doesn't feature whalers, being set in the Mediterranean -- The Far Side of the World is the tenth book in the series, and it does feature HMS Surprise being sent to intercept USS Essex the fictional USS Norfolk, meant to be representative of the Essex, which was turned into a French ship in the movie.

Anyhow ... I've read the book more times than I can count -- I generally read the series at the start of the summer, and I turned 45 this year, but I can't immediately recall the book Aubrey insisting that his men become lubberly (this comes up in other books in the series -- I remember untidy reef-points and a bit of filth on the masts). I think the movie Aubrey attempts to make the Surprise look like a whaler, possibly by adding in a crow's nest, which I've always thought to be one of the more implausible parts of the movie; Surprise is always said to be recognizable by it's thumping great 36-gun frigate's mainmast.

To get to the heart of your question, though, it's not that whalers are thought of as particularly lubberly sailors, but that the Royal Navy took enormous pride on being utterly professional in how it conducted itself. Crews were fairly enormous for the size of ships they were on, and in the time-honored tradition of militaries everywhere, officers made work for the men in keeping their ships spic-and-span.

Men in the RN were turned up before dawn to scrub the decks with holystones and rinse them with water before swabbing them dry, every day (there's a good line in Post Captain about Aubrey's retinue being horrified that his house was turned out only once a year, rather than daily). Sailors in the RN were expected to splice damaged lines, rather than knotting them; to keep loose lines faked down instead of leaving them in piles on the deck; to keep their standing rigging taut; to keep the paintwork neat; and so forth.

Whalers, with their much smaller crews, didn't have the manpower to do that, and in any case their profession depended on having a large try-works so they could strip the blubber off a whale's body and render it down, a process that would produce an indescribable amount of filth aside from the dirty smoke from the furnace (after the first firing, the fritters from the blubber would be used as fuel).

The other main difference in the professions, of course, is compulsion -- whalers signed on for a portion of the profit from the voyage, and discipline was more relaxed on a whaling ship than on a RN ship. Although whalers (and merchant seamen in general) could and did accept corporal punishment for crimes at sea, there was nothing like the system of discipline in the Royal Navy and the implicit compulsion to do the work of keeping a ship tidy and taut.

I've written a lot more about this if it's of interest.