Deuteronomy 29:29 (The secret things belong unto the LORD our God: but those things which are revealed belong unto us and to our children for ever, that we may do all the words of this law) has been a very powerful passage for the institutional church, allowing it to dismiss many troubling Bible questions, claiming that the answers are unknowable. That claim coupled with the obvious emphasis of the Bible on faith has conveniently diverted many honest truth seekers from challenging the church's longstanding doctrines.
In relying on God's mysteriousness as noted, the church contends that God's intelligence is so much superior to ours that we cannot comprehend His thoughts and motives. He is too righteous and majestic to be defined by human thought and reason. This church portrait of God is apparently designed to project God as majestic and omniscient, far above the limitations of man. Most would admit that majesty and omniscience should characterize God, but then so should fairness, equality, and uprightness. One without the other is starkly inadequate to maintain the respect of the human heart, as misguided as that heart may often be.
If, in fact, the human mind has such a weak grasp of what is morally, ethically, and logically right, as the church suggests in its depiction of God, then how can we trust ourselves to participate correctly in our own salvation? The church claims that our minds have been distorted by a combination of our depraved nature and Satan. Thus, in response to troubling questions about God's own nature, words, and actions the church falls back on the claim that God is just unfathomable to the human mind and right by definition no matter what He may do. Seemingly, a mind so incapable of right reasoning and correct comprehension could not be trusted to decipher the puzzle of scripture and make the fateful decision Orthodoxy demands in order to be accepted.
As I have said before, God is undeniably full of mystery, and that mysteriousness can result from a limited human capacity to understand the unknown at this time and in the physical realm. However, it is inconsistent and totally incomprehensible to teach of a god who establishes ethical and moral principles for mankind which He then violates with magisterial impunity.
I believe the mysteries of God are real and marvelously so. The counter intuitiveness of these mysteries is mirrored in the corresponding strangeness of many recent scientific discoveries. However, I cannot accept that God's mysteries can explain and potentially justify the horrendous and totally unfair and unequal eternal destiny projected by the doctrine of eternal punishment, for instance. In particular, I don't believe that at some point in the future I will understand how God justified genocide in the Old Testament, if the result of that act was eternal damnation for all those who were slaughtered. Some may muster the "faith:" to accept that as a possibility, but my "faith" is just not that strong, I guess.
To repeat myself again, the mysteries of God point mankind to something hidden but marvelous, in my mind. They are not intended to mitigate the bad taste of church doctrine or to provide a covering for God's apparent disregard for all human moral sensibility.