Okay, so it's late, so I'm gonna keep this short. But I'm gonna ask you a few questions and ask you to think through them critically, because I believe your answers to them will radically affect your beliefs...let me rephrase, they do radically affect your beliefs, this will simply aid us in identifying this circumstance. When we read the Bible we often come up with questions. This is good, and healthy. Questions encourage thought and when we question and subsequently find answers our thoughts are more firmly established, faith is built, etc. But there are times when we come to Scripture and are troubled by what we find. Times when God exercises speedy justice and we question His fairness. Times when we see something go unpunished and question His justice. Times when we come up against a doctrine (eg, predestination) that seems to contradict our view of who God is and/or how He operates. In times like these it is of extreme importance to keep in mind that things such as love, grace, justice, mercy, holy, and other words we use to describe God are just that descriptive. Our words do not constrain Him. Even when He uses a word to describe Himself (eg, holy) we ought to remember that He defines it, it does not define Him.
I suppose my pint here is this. By all means question. People who are afraid to question are afraid of the truth. Many great men in the Bible from the prophets, to kings, even Jesus Himself questions God the Father. There are things of God that we will not understand this side of glory, and others that we will only understand when we honestly and deeply question and take those questions to God Himself. But be prepared for the answer you will receive. God will not change for us. But we are obligated to change in light of who we are and who He is calling us to be. That is where nearly all honest questioning leads. A heart change that leads to life change.