[Click here for the previous article on The Perspicuity of Scripture.]
Something that helped me with this question was a section in Erwin Lutzer's book Doctrines that Divide. Lutzer lists four of the reasons why Christians don't agree: the limitations of men, the perversion of man, the unbelief of man, and the traditions of man. These are problems that each of us should recognize.
The Limitations of Men
There are some doctrines that are difficult simply because human beings are limited in our knowledge and understanding. For example, discussions free will are notoriously difficult. The Bible is clear that God is sovereign over everything and that humans are morally responsible for their choices; but how to put those two truths together is a paradox. We simply don't have enough insight to understand how that works. We lack information and we lack mental ability. Our three-pound brains simply do not have the computing power for some problems. In addition, there are other truths that remain mysteries to us because God has not chosen to reveal them to us.
The Perversion of Man
What Lutzer means here is that we often twist the meaning of Biblical texts to suit our own desires or biases. We want something to be true, so we read the Bible in a certain way. This category doesn't merely include issues dealing with sexual perversion, although that would be one example. You need to work very hard to bend the Bible enough to say that sexual relations are blessed for anyone besides a husband and a wife who are married to each other. Yet, people write books to argue that. Of course, there are countless other examples of this category besides sexual issues. Sometimes people know full well that they are twisting Scripture, but often they want to see something in Scripture so badly that they see mirages.
The Unbelief of Man
Some people have a naturalistic worldview that absolutely rules out any involvement from God. There is no way to believe all of the Bible's teachings related to science, creation, prophecy, history, and miracles if you start with a precommitment to naturalism. The Bible is not anti-scientific, but it does include the core idea that God exists and that He can interact with the created world. For various reasons and pressures, some people refuse to accept that. Many professing Christians have been influenced by naturalism to one degree or another. There are Bible commentaries built upon a foundation of unbelief. It is a mistake to let our worldview shape our view of Scripture instead of letting Scripture shape our worldview.
The Traditions of Man
We all have inherited certain traditions about what Christians should believe. The only difference is that some people recognize their traditions and some people are blind to them. The person who says, "I have no traditions" may be like a fish that doesn't realize that it swims in water. In truth, many of our disagreements boil down to the fact that we swim in different ponds with different accepted beliefs. There is often little incentive to reexamine these beliefs, especially if it might mean having to find another pond.
In addition to these, let me add a few more:
The Desire to Please Men
We usually think about "traditions" being something old, but in reality any influence we have from the people around us can distort our view of God and the Word. For many people today, the new "tradition" is the desire to be seen as progressive. People want to be judged well by their peers. No one will be true to God's Word who craves the approval of the world.
The Failure of Men
Many Christians have no idea what they should believe because they are Biblically illiterate. Many churches have failed at discipleship. Many pastors have failed to faithfully preach God's Word. Many parents have failed to instruct their children. And many Christians have failed to take responsibility for their own spiritual growth. (Sorry to be so negative here! I wish I were wrong.)
Beliefs are connected. One wrong belief often affects another. For example, if you have a low view of God's holiness, you will have a shallow view of man's sin. If you have a shallow view of man's sin, it would be difficult for you to see why sin is so awful that God should punish it with eternal condemnation. It would be difficult to see why it was necessary for the Son of God to come as a sinless sacrifice to pay an infinitely horrible price as our substitute. You see, false teaching leads to a chain reaction of error.
In conclusion, there are many reasons why professing Christians disagree. All of these reasons have one common core: man. The reason Christians disagree is not because God is a bad communicator. The problem lies with us.
[Note: The four original main points are from Lutzer but the comments are mine.]
See also: The Perspicuity of Scripture; and How to Silence God on a Subject You Don't Like