Biblically, see the first chapter of Genesis, that all that God created was "very good." Thus, the entire world is good, even when we don't realize it. And Psalms 144 states: "God is good to all..." There are others.
Philosophically, the apparent existence of evil is in order to allow us free choice, to overcome evil and thus attain the ultimate good, which is the good of earning our reward, instead of having it handed to us for free.
Regarding our inability to understand suffering, imagine a little child at the dentist: All he knows is that the dentist is hurting him. Can the child understand that the dentist is actually a good man and is trying to save him from future pain? One day that child will thank the dentist.
This is a very short, condensed answer, and there is much more to be said on this subject.
