I think it comes from compassion and empathy, but also from the common sense in recognizing that it can't be good to cause harm, "horror", and/or destruction in one's own or someone else's life; but also from the belief that one "tiny, human-being, of a creature", within the scheme of "all of life" and "all of the world", has no right to inflict destruction or destructive elements on others or into life in general.
So, I think it's more a matter of the evolution of man's increasingly enlightened mind when it comes to the way evolution moves things in a more advanced direction (and direction that favors life, rather than destruction of it); and the belief/awareness that what's in keeping with Nature and/or the natural order of things (and evolution) are "good"; while things that go against them are destructive, out of line with Nature, and therefore "evil".
I think that as man has become more and more capable of higher thinking (a lot of people aren't there yet, but that's a subject for another time), the simple concept that human beings should not make life on Earth a "hell" (especially since so much pain is often caused when Nature does her thing, like bring ice ages and massive storms and death to individual creatures). I think it's in human nature to accept what no human being can do anything about, but I think it's also in human nature to see pain and suffering and try to sort out whether it was caused by the actions of any human being(s). I think when it comes down to it, "good" and "evil" amount to what makes a positive contribution to life in general (or at least doesn't take away from it) and what is intentionally and/or carelessly destructive in this world.