The old, and much debated, question of why a benevolent and omnipotent God would allow suffering has many answers, but there is a more intuitive grasp of one answer to be found in works of fiction (at least one by an atheist).
There are two series of books which I know of which revolve around extremely powerful creature benevolent towards humanity. They are not omnipotent, and far from perfectly good (in fact ready to commit genocide of non-humans for little reason), but they are able, and wish to keep humans completely safe and comfortable. The creatures are Isaac Asimov’s robots and Larry Niven’s protectors.
In both cases they decide to allow humanity to live and develop without their constant presence and intervention — although both decide to intervene subtly without revealing themselves too openly. Sounds familiar?
They do this because human beings need to be able to develop. In Asimov’s books human world’s that use robots gradually die as their culture fails. Niven’s protectors decide that humans do not want or need to be cosseted.
The result is immense suffering, but no one reading either series could say that they would prefer to live in a world in which they were looked after by robots or protectors.
I will not go into the details (those who want them can read the books), but looking at the problem this way can make the argument that we need to live with our choices and their consequences more comprehensible.