@rattler: The difference is that unlike with cows or deer, whaling is a significant threat to the already diminished population. The whale population today is something like 10% of what it used to be, and not all because of whaling but also because of climate swings, development of breeding grounds, etc. The whales the Japanese kill are a threatened species and protected in every other country except for Japan -- where, unfortunately, there seems to be a good number of them.
If whales went extinct, the effect on the oceans would be devastating. Without whales (which consume massive amounts of krill), the krill population goes waay up, causing the phytoplankton (which krill eat) to decline. phytoplankton is the bottom of the food chain, so every animal that eats the phytoplankton and every animal that eats the animals that eat the phytoplankton are affected. Kill a deer, and there are always more. They're in no danger of becoming extinct at the present, and there are laws limiting the number you can kill per year (I think; you would know.) The whaling off the coast of japan is unregulated slaughter.
@NepAK: Unfortunately you're right. It's perfectly legal for the Japanese to whale as long as it's for so called "scientific" purposes. But if you ask me no "scientific purpose" is important enough to risk wiping out an entire group of threatened whale species. As for "It's part of their culture," I don't know about you but I don't want to see whale species go extinct so the Japanese can keep their cultural traditions. They can eat venison, pork and beef like everyone else!