If the religious question is: how can it be that people created by a good God can do cruel things? then the secular question...is: why should the human animal, created by no deity, driven by sex and survival, be kind?Adherents to various religions will have their own answers. As for the secular question, the answer is not such a mystery: compassion and altruism are 'wired' into the behaviour of highly social animals such as humans (see Hrdy, de Waal etc). 
No, the real question is how to manage the kindness 'instinct' with reason and imagination. Adam Smith (a deist, perhaps) argued the limits were clear:
The administration of the great system of the universe ... the care of the universal happiness of all rational and sensible beings, is the business of God and not of man. To man is allotted a much humbler department, but one much more suitable to the weakness of his powers, and to the narrowness of his comprehension: the care of his own happiness, of that of his family, his friends, his country.This may have seemed adequate in 1759 but it will not do today. Our comprehension may still be narrow but our responsibilities -- as a species profoundly impacting the biogeochemical cycle, extinguishing vast numbers of life forms and ready at a moment's notice to let slip the dogs of nuclear war -- are much increased. Our biggest challenge, perhaps, is to imagine more fully things we cannot directly see. 
Photo: Hans Scholl, Sophie Scholl and Christoph ProbstFootnotes
 Marcus Aurelius got straight to the point: "Waste no more time arguing what a good man should be. Be one!"
 This includes longer-term trends underlying short term blips.