It's a little of both. Officially, it's "scientific research", which everyone knows is BS. To many Japanese, it's based on the "cultural tradition" idea--they've always eaten whale meat and don't want to stop, depleted populations and clear evidence that these are highly intelligent mammalian beings notwithstanding.
There's some argument that whale provides a protein source that is otherwise unavailable, but nobody's particularly buying that. It's true for the isolated Inuit people in the high Arctic, who take a few whales a year. It's not true for a highly industrialized, technologically advanced nation at the crossroads of Asia, and doesn't justify taking thousands of whales a year.
As to commerce, well... somebody makes money off this, and some fishers are employed in the whale hunt, but I doubt that the Japanese economy would collapse without whaling. I think that it's basically just sheer stubbornness and racial pride, which is the big Japanese neurosis (for the record, I'm 50% Japanese-American); they're as bad that way as the British were in their heyday (and somewhat still are).
I'd call it the Japanese equivalent of Chimpy's obstructionism on global warming (also Steve Harper's, our asshat Canadian prime minister). There's no rational or intelligent explanation; it's just what they do. A plague on all their houses.
