The biggest problem is Sunni Arab domination, and the historical role of the army in Iraqi politics. The Iraqi army has been the bedrock of Sunni political power for centuries (before 1918, many Sunnis served as officers in the Turkish army, and assured the loyalty of garrisons in Mesopotamia.) After the British left in the 1920s, the army quickly became the power behind the monarchy, and in 1958 did away with the monarchy entirely by murdering the royal family. If the Iraqi army had been left intact in 2003, most Iraqis would have seen it as the beginning of the return of Sunni domination, if only because most of the officers were Sunni. Many officers may not have been loyal to Saddam, but they were loyal to Sunni domination. The army had to be disbanded. But that did not solve the problem of Sunni domination.
There are currently some 200,000 Iraqis under arms. The problem is that the "supervisory class" in Iraq has been, for centuries, largely Sunni. Recruiting and training police and security troops was done in haste to get these guys on the job, and on the payroll, as quickly as possible. There were not enough non-Sunni with any police or management experience. You have plenty of entrepreneurs in Iraq, but a real shortage of modern, reliable managers. The corruption is pervasive and leads to a rather different style of management, one that pays more attention to the managers welfare than that of the society as a whole. Most of the guys who know modern management techniques are Sunnis, and often former (or even current) Baath Party members. Since Saddam took over, guess who was favored when it came to college admissions, or study overseas? If you let too many Sunnis back into the management positions, guess who is going to have a great deal of control over the country, way out of proportion to their numbers? The Shia and Kurds notice this, they constantly look for then, and get very upset if they see the Sunnis sneaking back into power.
Nearly all the violence in Iraq is coming from the twenty percent of the population that are Sunni Arabs. Thousands of violent Sunnis have been arrested and interrogated and its pretty clear from those interrogations that the violence in Iraq comes from several sources. There are the members of Saddams security and intelligence organizations carrying out a pre-war plan for creating violence and disorder if Iraq is occupied. There are also many Sunni Arabs acting on their own to oppose those foreigners who would allow the majority Shia and Kurds to rule the nation. And then there were the foreign fighters, who saw Saddam as a great Arab hero and the Sunni Arab cause worthy of support.
And then there are some less violent habits and customs in Iraq which make rebuilding the country and establishing a government very difficult. The biggest problem is corruption in public and private affairs and the large number of Iraqis who will not take responsibility for their actions. These self-destructive customs has been around for a long time and result in a general lack of personal responsibility for corrupt acts. For too many Iraqis, the national mantra appears to be Its not my fault, its your fault. Iraqis steal public money, fail to carry out public and private duties, and then lie about it, or insist they were forced to do it by "others." Keeping everyone honest is a huge problem. While many Iraqis are reliable and honest, they are often opposed and sabotaged by those who are not. All too often, the honest and responsible Iraqis are outnumbered, or outgunned, by more corrupt, and violent Iraqis. The Sunni Arabs have made corruption a government tool, backed up by a readiness to use violence on those who do not want to make a deal.
While many Iraqis profess support for the nation of Iraq, its largely words, not actions that are being offered. Family and tribe are more important than any sense of working for the greater good. This is not an unusual attitude the world over. In all those countries where clean government is largely a myth, people look to family and tribe (extended family) for protection. This means that honesty and reliability is for the family, while anything goes for the world beyond.
Iraq has another problem that soldiers and reconstruction workers have to deal with. Theres a tendency to allow emotions, rather than logic and analysis, drive Iraqi public opinion and policy making. Rumors and the most outrageous stories spread rapidly and are readily believed. This is actually quite common throughout the Arab world. Go to an English language version of an Arab news outlet and youll see it in action. Actually, the English language versions tend to be a little more objective and accurate than the Arab language ones. The English language versions are usually done by Arab journalists who are bi-cultural because of being educated in the West. These journalists have to operate in two quite different worlds of truth and reality. The American side tries (not always successfully) for objectivity and accuracy in reporting. In the Arab world (and many other parts of the world as well), the party line, and a desire for the most exciting and shocking spin on a story, come first. This kind of journalism makes the fall of Saddam Husseins government into a great tragedy. It leads to inventing an endless litany of fictional American atrocities against Iraq. At the same time, the dozens of Iraqi torture videos discovered in Iraq, showing Saddams secret police at work, were rarely broadcast by Arab media outside Iraq. These videos were very popular inside Iraq, but foreign Arab news organizations shunned them because the reality of Saddam's atrocities did not agree with the fantasy of Saddam the Arab hero that these news outfits were pushing. Actually, the disconnect between reality and Arab news organizations (especially satellite news outfits al Jazeera and al Arabia) has become so great that Iraqis (according to a recent survey) are switching more to local TV stations. Too many Iraqis have been witnesses, or even participants, in events that were completely distorted by Arab media (as in American troops coming to help with something, like a small fire, and that visit being described by al Jazeera as some kind of invented atrocity). But many Iraqis do believe the propaganda, and that results in rock throwing, refusal to cooperate and other self-destructive behavior. Truth is not an abstract, lack of it can kill in places like Iraq.
The real enemy in Iraq is a handful of historical conditions and national characteristics that created Saddam Hussein and the current difficulty Iraqis are having governing and rebuilding their country.