*sigh* No offense to anyone out there, but animals are unintelligent, therefore humans, as the only intelligent life on this planet, are well within our rights to eat them. Does that mean we should keep them in factories where they never see the light of day?

No.

For one, that prevents the animals from getting vitamin C, which a deficiency of can harm the quality of produced goods.

Second, most indoor factories tend to be badly ventilated, which can harm the quality of produced goods, as said before.

Thirdly, animal abuse that results in lasting physical injury results in, again, decreased quality of produced goods.

So long as the animals are properly nourished, through direct feeding or even more basic of needs, they are being taken care of responsibly and correctly.