Principle number 28 of Basic Elements of Islam: The message in a standard Quran is difficult to decipher. Whether it was done intentionally or not, the Quran's message has been scrambled and in a sense, coded. This discourages almost all non-Muslims and a significant percentage of Muslims from understanding it.
In what way is the message scrambled? First, the chapters are published out of order in every standard Quran. Rather than printing them using the chronological order in which they were revealed, the 114 chapters (suras) of the Quran are arranged using a baffling method: They're arranged in order from the longest chapter to the shortest. That's the traditional order.
When you read a standard Quran straight through like a normal book, the message is disjointed and the story jumps around and seems contradictory. One very important consequence of this curious disorder is that it hides the clear progression from Mohammad's semi-tolerance of non-Muslims to his violent hatred toward them.
The disorder also prevents anyone from figuring out which passages are abrogated unless they know the chronological order of the Quran.
The second way the Quran has been put into code is by putting the key somewhere else. Much of the Quran cannot be understood without being familiar with the life of Mohammad (by reading the Sira and the Hadith). These are primarily about Mohammad — what he said and did.
In other words, the Quran — the source book, the single most important holy book in Islam — can't be understood without the key, and the key can only be found somewhere else, which is similar to one of the ways a message can be written in code: Put the key to understanding the message somewhere else besides including it in the message. This is enough to keep most non-Muslims from understanding the Quran, and also keeps most Muslims on a need-to-know basis. So the only ones who really know what's going on are the imams and the scholars. They call the shots. Everyone else is in the dark.
If the Quran wasn't put in code deliberately, it has been a tremendously fortuitous accident which has served the goals of Islam very well throughout history. Fortunately, someone has unscrambled the Quran for us. Read more about that here.