In Iraq, the United States is attempting to co-opt the only groups with any legitimacy to much of the Sunni population by forming alliances with and arming Sunni tribes and insurgents.
The Sunni groups we are arming are, at least in Al Anbar, the groups with the most political legitimacy. The official government of Iraq has no legitimacy and no power, and hasn't for months if not years. Our presence has no legitimacy and little power - we can destroy, but we cannot create. Al Qaeda in Iraq is in a similar situation. That leaves the Sunni insurgents and the local institutions that they are tied to (rather than thinking of the insurgency infiltrating local governments, it makes more sense to see both the local governments and the insurgencies as receiving their strength from the same source, the consent, freely given or not, of the local population).
Looking at the Iraqi provinces, it makes sense to strengthen the hand of those organizations that are going to face the least resistance from their local populations, and if you can create tactical alliances with American forces, so much the better. Absent the tactical alliances, then arming the Sunni tribes/insurgents simply becomes a method of effecting our withdrawal and ensuring that there isn't a vacuum behind us (if that were the case, this might be a good scenario to use Nagl's Advisory Corps).
The problem comes when you look at Iraq as a whole. If (likely when) the Sunnis we help are unwilling to give up their maximalist objectives of control over Iraq, the civil war will intensify, as Sunnis will be able to focus their resources away from fighting a three-front war (against Al Qaeda, the USA, and Shi'ites) to fighting only Shi'ites after Al Qaeda is defeated with American assistance, and then America leaves. That would mean that out of the chaotic situation now in Iraq, we'd be creating a Sunni pole that may eventually unite against a Shi'ite pole (if the Shi'ites stop fighting each other for long enough). In such a conflict I think it'd be more likely that neighboring states would intervene, because the actors would be more familiar-looking. We'd be substituting the choatic "open-source" violence for more organized yet potentially widespread violence.
It is a risky trade-off. One risk is that Al Qaeda in Iraq will be defeated quickly, and Sunni insurgents will then refocus on killing American soldiers with their American weapons. However, as it should be clear by now, the United States is unable to cleanse Iraq of the Al Qaeda presence it has brought by itself, and so the risk may be worth the reward of an Al Qaeda-less Iraq.
The Sunni tribes/insurgents could probably get rid of Al Qaeda in Iraq by themselves if they put their minds to it, but in the current environment they'd be foolish to do so. Focusing on Al Qaeda would decrease their focus on killing Americans, which is a large part of why their power is accepted in their communities. It could also conceivably leave them weaker in any eventual showdown against Shi'ites.
This post is too long already and I want to go to bed. My last thought is this: that this whole train of thought only makes sense if you view the American presence in Iraq as something worth preserving indefinitely. In that case, American troops would be able to either turn on and eliminate the armed Sunnis after they've done their job of eliminating Al Qaeda, or, if the Sunnis give up the goal of dominating a unitary Iraqi state, they could aid the Sunnis in creating "Sunnistan," a largely independent Sunni area of Iraq that would have its own military force (like Iraqi Kurdistan has the Peshmerga). If you think American troops should just leave, as I do, then this policy is misguided. It will prolong the Sunni/Shi'ite civil war by arming the weaker party in that conflict, prolonging the time that it takes for the Shi'ites to crush the Sunnis in Baghdad. Prolonged aid to Sunnis, driven by our desire to appease our Sunni allies outside of Iraq, could convince the Sunnis that their maximalist objectives are feasible, and thus "perpetuate a state of war indefinitely by shielding the weaker side from the consequences of refusing to make concessions for peace."
We shouldn't even be in this situation.