Killing animals and eating them are both acts that produce traits of wickedness in the soul. God commanded the first man to eat only plants, and no meat. Even when meat was later permitted, only certain types of meat were allowed to the Jewish people, and even this was out of necessity alone.

Eating meat desensitizes the soul:

Apart from the fact that killing animals involves cruelty and rage, teaching people the evil trait of spilling blood for no reason, eating the meat of some animals also causes coarseness, murkiness, and insensitivity in the soul. As the verse explains at the end of the passage that prohibits some animals to the Jewish people, “And you shall not be rendered impure by them, and become impure [venitmetem] through them” (Leviticus 11:43). The letter alef is missing [from the word venitmetem, rendering it similar to the word atimut, insensitivity], to teach that eating non-kosher animals causes coarseness and insensitivity.

The first man ate only plants:

As a result, even though the meat of some animals is edible for human beings, God preferred to withdraw the small amount of good that comes from eating meat in order to avoid the evil and great harm that could arise from doing so, and He therefore prohibited the consumption of meat. He compensated for the foods that he removed, by designating, especially for humankind, edible food from plants, such as wheat, barley, and everything that contains seeds that may be planted, including the fruit of the trees. To the rest of the animals, He gave “all green vegetation” (Genesis 1:30), rather than seeds that can be planted, and this [fact, that humans eat food that they grow from seeds while animals eat merely “green vegetation”] indicates the superiority of humans over other animals.

The consumption of certain animals was allowed out of necessity:

When the Torah was given to the Jewish people…it prohibited eating those animals that cause coarseness and murkiness in the soul. Even with regard to those which were permitted, the Torah spoke only in response to the evil inclination [to eat meat]. (Rav Yosef Albo, Sefer HaIkkarim 3:15)

One must have compassion for all creatures and not treat them with contempt or allow them to be wasted. Uprooting a plant or killing an animal is permitted only in order to elevate the object from the level of vegetable or animal, namely, to make it part of a human being.

One must have compassion for every creature as much as is possible:

One’s mercy must be upon all creatures; he must not treat them with contempt, nor destroy them [needlessly]. For divine wisdom is extended to all of creation: mineral, vegetable, animal, or rational [human beings]. For this reason, we are forbidden to treat food with contempt. Just as the divine wisdom is not contemptuous of anything that exists, and is the source of everything, as it is written, “In wisdom, You made them all” (Psalms 104:24), so too, it is appropriate that a person’s mercy be applied to all of God’s works…. As a result, one should not treat any of the creations, all of which were created in wisdom, with contempt. One should not uproot any growing thing unless it is necessary, and one should not kill any animal unless it is necessary, and he should ensure that [any creature he does kill] receives a good [quick] death, with a knife that has been checked, in order to be as merciful as he can.

One may use means that appear cruel only in order to elevate things:

This is the principle: One must have compassion for all creatures, and must not cause them any harm; this stems from wisdom. The exception is in the case of an act that elevates something from one level to the next, such as from vegetable to animal [when an animal eats a plant], or from animal to speaker [when a human eats the meat of an animal]. In these cases, it is permitted to uproot the vegetable or to kill the animal. A person causes the object’s loss in order to bring about its gain. (Rabbi Moshe Cordovero, Tomer Devora 3)

The Torah allows the consumption of meat, but states that it is permitted only because we have not yet reached a high level of morality. In the future, we will achieve a purer morality and will append to the Torah’s commandments the moral imperative to refrain from eating meat.

We eat meat because of our low moral level:

When the Torah permitted the consumption of meat after the consecration of [Israel through] the mitzvot at the giving of the Torah, it presented an extended description: “And you say: I will eat meat, because your heart will desire to eat meat; with all your heart’s desire you may eat meat” (Deuteronomy 12:20). There is a subtle rebuke and the indication of a limit. In other words, [the Torah permits eating meat] as long as your inner morality does not cause you to be revolted by the consumption of the flesh of animals as you are already revolted by human flesh. The Torah did not need to give an explicit prohibition against [eating human flesh], as one does not need to be warned against that which he already knows intrinsically. [Intrinsic moral prohibitions of this sort] are equivalent to explicit ones. When the time comes for human morality to abhor the flesh of animals because of the moral repulsion it involves, then you will not desire meat, and you will not eat it.

When humanity reaches a perfect state, our relationship to animals will change:

When humanity reaches the objective of its bliss and complete freedom, when it reaches the height of perfection of the pure knowledge of God, and the holiness of a life that is full in its character…humanity will realize, with regard to its fellow creatures, the animals, what is fitting from the perspective of pure morality. There will no longer be a need for concessions of exigency, for the compromise between the attribute of compassion and the attribute of justice with respect to the individual, or concessions where the Torah spoke [i.e., permitted something] only because of the evil inclination. Instead, he will walk on the path of absolute good. (Rabbi Avraham Yitzĥak HaKohen Kook, Ĥazon HaTzimĥonut VehaShalom)

Further reading: For more on the proper treatment of animals, see A Concise Guide to the Sages, p. 435; A Concise Guide to Halakha, p. 613.