Animals need to be protected, but make no mistake – they were put on this earth to serve MAN, not vice versa. That said, we DO need to be makpid on tzaar baalei chayim, and that is why we have so many halachos that revolve around that hashkafa, i.e. kilayim, feeding one’s animals before eating one’s own meals, making sure to milk the cows on time, and possibly (though we are not allowed to say it is THE reason), shiluach hakein.
The whole sedra of Noach, teaches us a lesson about responsibility towards animals, but it likewise gives us the reason why animals were now permitted to mankind for consumption, though within boundaries. Ultimately, they are here for OUR benefit and use, and Man has dominion over them, according to Hashem’s own words.