A lot of people try to pawn that off on free will when evil acts are not prevented by god. But what of the free will of the victims, it isn't their will to be raped or murdered, etc. So if god doesn't intervene in such acts, it is viewing the will of the rapists as more valid than that of the victims. Even better, god could arrange it so that these criminals experience some sort of event that changes them and makes them lose the desire to harm others, and even I stills the desire to help prevent future rapes and murders, rather than just dumping these people in hell.
In reality, suffering happens.
Should God, and would God, are irrelevant questions. Should we, and would we, are relevant ones.
Should we rape children?
Should we perpetuate pointless arguments on the merits of omnipotent Gods existent outside time and space and simultanesously within it which we don't believe in having more motive for creating a non-suffering Earth than the suffering one that exists, as if we might be able to understand the motives of whomever that God is we don't believe in?
Or should we accept the suffering Earth and the desire of all people to be free of suffering?
For the christian this is seen in Jesus' quotes 'love your enemies' and 'consider others as yourself'.
For the atheists, in the realization that suffering (rape, murder, death, torture, whatever it may be) is an awful, undeniably violating thing that is best off alleviated and avoided.
We're all after the same purpose here, the same things; to be happy and to be free of suffering. One person here chooses the path of the God they believe in, whose Son taught people empathy and consideration for others.
Another person believes in the inherent value of another's happiness and right not to suffer.
It is important for us as a species to draw these similarities and commonalities and even if we don't agree with one another on the dogma or the back-story, work towards what we all realize is inherently our biggest innate desire - to be free of suffering at no expense to another's freedom from suffering.
If anybody is to speculate further, it may well be a good idea to accept that suffering happens and use the reality of the Earth as some basis for speculating on the existence of God, rather than say 'no God exists because if he did we wouldn't suffer'. That is as much a massive jump in logic as anything else, although it does underpin perhaps a belief in 'something out there' that isn't the christian God, even if that 'something' is just an ideal of ultimate morality. That may be intrinsic, and perhaps instead of using it against the teaching of a morally enlightened character like Jesus who went round healing and giving, you should follow its call and become what you really believe.