Before December 2006, when the gloves apparently came off at least a little for the Bush administration, they appear to have decided not to retaliate overtly against the Iranians for the support we knew they were lending to anti-coalition operations in Iraq. So the administration used the "might be rogue elements operating outside Tehran's control" subterfuge to throw the press off the scent of what it knew perfectly well was Tehran's complicity, passive or active, in the attacks against American soldiers in Iraq. Since December, the U.S. has been a lot more aggressive towards Iran, cruising huge naval armadas just a few dozen miles from Iranian naval bases without prior notice; detaining hundreds of Iranians and Iranian proxies in Iraq; hammering Iranian-backed militias in Iraq, etc., etc.
In a sense, we may have been storing Iran's transgressions in the bank until the day we could cash them in to justify overt action against Iran. This only makes sense from a strategic point of view. I am all for deterrence, but deterrence presumes two conditions that do not obtain in the case of Iran: (1) that the adversary wants to avoid conflict, and (2) that the adversary is under unified control. Then there is the question of containment theory. If you retaliate automatically for every transgression at the moment the transgression is committed, you let the enemy control the timing of conflict, and you thereby concede to him the initiative. This is the criticism that John Lewis Gaddis levels against several postwar administrations — most of all Kennedy's — in his classic Strategies of Containment. Much better to wait until the moment of our own choosing to take the action most appropriate to achieve our lasting strategic aims.
Moreover, just because we haven't retaliated overtly doesn't mean we haven't retaliated covertly. We may well be fighting fire with fire — and in fact, Iran openly accuses the U.S. of doing precisely that. And let's not forget that the administration is not looking at Iran's terrorist activities in Iraq in isolation from the other things going on — including Iran's shifting political strategy in Iraq, and the diplomacy of the nuclear issue.
This is a complex web, much of which lies in the shadows of classified information and covert operations. U.S. policy is likely to make more sense in hindsight than it does now.