The problem is the concept of the almighty God, the omnipotent, all-knowing and always-right entity that is the creator of everything. I personally disagree with many decisions he makes in the Bible. For example outcasting Adam and Eve and punishing them in a seriously gruesome manner. It always looked to me like he had a serious anger management issue. Or when he talked JJ Abrahams into attempting to kill his own son as a "test of faith". Or when he picked a group of humans that he liked and decided that all others that he didn't like can be exterminated at will. That God is a terrible, terrible character that ABUSES his power on several occasions. I personally think that we, humans, in general behave morally superior to the God described in the Bible. How dare I?
At the same time he's also supposed to be all-loving and all-forgiving. But that clashes with the concept of Hell and all the stuff God did to punish and exterminate people who happened to disagree with him.
I guess faith is the ability to overlook all these contradictions. If the Bible says Earth and men were created in 6-7 days, but science says Earth is 4 billion years old, then the Bible just must be right.