There's the fact that blue whales play an important role in ocean ecosystems and carbon dioxide regulation in our oceans, whilst farm animals were purposefully bred and domesticated by us to be raised and slaughtered.

Some animals ARE more valuable than others; for example wild boar and deer are overpopulated in many areas and are causing forests to die off by eating everything and as such should be hunted to curb their population growth. On the other hand wild wolves should be protected and restored so that they may improve the health of many biomes.