In 1300 AD cruelty meant a very particular thing: the opposite of clemency. What we presently call cruelty was called brutality, and there was a clear distinction:
...cruelty is nothing else than sternness in the exaction of penalties. Rational abatement of penalties is an act of equity, but the sweetness of disposition that prompts such abatement belongs to clemency: so also excess of punishment, so far as the outward act goes, is an act of injustice; but as for the austerity of temper that makes one forward to lay on increase of punishment, that excess belongs to cruelty. Mercy and clemency agree in both of them shrinking from and abhorrin the making of another miserable: but to mercy it belongs to relieve misery by the bestowal of kindness; to clemency to diminish misery by abatement of penalties. And because cruelty means excess in the exaction of penalties, cruelty is more directly opposed to clemency than to mercy.
...brutality, is so called from the likeness that it bears to wild beasts [that] hurt to men in order to feed on their bodies, not for any cause of justice, since the consideration of that belongs to reason only. And therefore, properly speaking, it is called brutality, or savagery, when in inflicting punishments a man considers not any fault of the person who is punished, but has regard merely to his own delight in the torture of his fellows. This is clearly a case of brutality: for such delight is not human but brutal, coming either from evil custom or from corruption of nature, as do other similar bestial proclivities. Cruelty, on the other hand, has regard to the fault that is in the party that is punished, but exceeds due measure in punishing. And therefore cruelty differs from savagery, or brutality, as human malice differs from that which is bestial.
http://oll.libertyfund.org/?option=com_staticxt&staticfile=show.php%3Ftitle=1967&chapter=124333&layout=html&Itemid=27 Cruelty is a product of rational mind: it is the injustice of exceeding the limits of just punishment; in contrast, brutality is the product of a [corrupt] animal soul. This distinction was already eroded in Montaigne's times, but still not quite. In his famous essay on cruelty
http://essays.quotidiana.org/montaigne/cowardice_the_mother_of_cruelty/Montaigne says that when people kill their enemies in order not to defend themselves from the actual offence, but out of mere revenge for past offences or, worse, preventively, that's cruelty. Cruelty is wrong, because dead people cannot suffer the humiliation of defeat and repent, which depreciates the value of one's revenge. Cruelty is a display of cowardice and certain corruption of spirit; Montaigne seconds Seneca in calling weakness the mother of cruelty. However, elsewhere he realizes that cowardice alone does not explain cruelty [and there he probably means Aquinas' brutality]
...I could hardly persuade myself, before I had actual evidence, that there exist any souls so unnatural as to commit murder for the mere pleasure of doing so; as to hack and chop off men's limbs, as to sharpen their wits for the invention of unusual tortures and new forms of death; and all this without enmity or gain, but merely for the enjoyment of the pleasing spectacle afforded by the pitiful gestures and motions, the lamentable groans and cries, of a man dying in anguish. This is the extreme limit to which cruelty can attain, "that one man should kill another, not in anger or in fear, but solely to enjoy the sight."
http://www.olearyweb.com/classes/philosophyS2/readings/montaigne/oncruelty.html He grounds such brutality in mistreatment of animals, which he explains by (i) the decline of a belief in metemphsychosis, and (ii) the impulse to inhumanity as implanted in our animal nature. However, there is an opposing impulse, too
...there is a certain consideration, and a general duty of humanity, that binds us not only to the animals, which have life and feeling, but even to the trees and plants. We owe justice to men, and kindness and benevolence to all other creatures who may be susceptible of it. There is some intercourse between them and us, and some mutual obligation.
Another 200 years had passed, and the idea that cruelty originates primarily in brutality to animals became the common currency, and it largely explains why there was an explosion of advocacy for kinder treatment of animals. It is not cowardice that is the mother of cruelty, it is perverted curiosity in little children reinforced by bad example. Here is Locke:
...I have frequently observ'd in children that when they have got possession of any poor creature, they are apt to use it ill: they often torment, and treat very roughly, young birds, butterflies, and such other poor animals which fall into their hands, and that with a seeming kind of pleasure. This I think should be watched in them, and if they incline to any such cruelty, they should be taught to contrary usage. For the custom of tormenting and killing of beasts, will, by degrees, harden their minds even towards men; and they who delight in the suffering and destruction of inferior creatures, will not be apt to be very compassionate or benign to those of their own kind. Our practice takes notice of this in the exclusion of butchers from juries of life and death. Children should from the beginning be bred up in an abhorrence of killing or tormenting any living creature; and be taught not to spoil or destroy any thing, unless it be for the preservation or advantage of some other that is nobler. This delight they take in doing of mischief, whereby I mean spoiling of any thing to no purpose, but more especially the pleasure they take to put any thing in pain, that is capable of it; I cannot persuade my self to be any other than a foreign and introduced disposition, an habit borrowed from custom and conversation. People teach children to strike, and laugh when they hurt or see harm come to others: and they have the examples of most about them, to confirm them in it. All the entertainment and talk of history is nothing almost but fighting and killing.
http://www.fordham.edu/halsall/mod/1692locke-education.asp Of course, Locke's thinking is self-contradictory: if cruelty is unnatural, then cultural habituation of children to cruelty (which he identifies as its supposed origin) should result in indifference rather than pleasure. So how could it become the source of pleasure? He does not explain.
That was the height of the Enlightenment, and we are well past this light.
In our own age, we are slowly graduating back to cowardice as the mother of cruelty. People (terrorists, tyrants, manipulators, criminals, torturers) are cruel because they are cowards - as if their bravery (which is often quite obvious) would make any difference. This is pathetic demonization of one's enemies. It fools no one, but repeated nevertheless, because any explanation is better than no explanation. Meanwile, it turned out that kindeness to animals is no impediment to killing millions of people. Our torturers and tyrants post the photos of their pets just like everyone else.
Modern pseudoscience
http://books.google.com/books/about/The_Science_of_Evil.html?id=ojWMEU2lQCoCoffers a wide range of "evolutionary" explanations of brutality that are not worth examining here for lack of any substantial insight; usually, it is a variety of an ingenous idea that cruelty is caused by the lack of empathy in the brain that is not properly wired. At best this "rationale" might explain what corruption of one's animal soul constitutes brutality; in reality, this description is so unspecific that one cannot seriously call it an improvement on medieval scholasticism. In any case, this is an "explanation" of brutality rather than cruelty, not that the authors of such books know about it.
I believe that no one had tried to explain cruelty for 500+ years; what was writen afterwards can be safely tossed out without much loss. It was expected that fusing brutality and cruelty into one notion would make it easier to explain it away, but (in my view) this approach has failed.
What is cruelty?