The risk on underestimating does also exist. But, with the exception of AQ's ability to pull off the 9/11 attacks, there is no history whatsoever of underestimating the attack capability of Islamicists. I'm not too worried about that. As far as the things they can actually pull off on a regular basis, there is no amount of military action that will stop a guy with a backpack from getting on a bus.
I guess you'd just prefer that we spend $1B a month or so thwarting overhyped threats. If one accepts the simplistic "we are just going to stop the threats before they arise" approach, there is no justification for not taking out Pakistan and Iran IMMEDIATELY. They both pose far greater threats than Iraq, because the threat of a "smoking gun appearing in the form of a mushroom cloud" is at least realistic in those cases.
The issue is far more asymetrical than that. Iraq was clearly a supporter of terrorism, had used chemical weapons in the past, had not complied with the terms of the 1991 cease fire regarding clear demonstration that they had destroyed their WMDs, was a destablizing force and was run by the worst of the pan-Arabist leaders. So there were plenty of reasons within the borders of Iraq to take out Saddam and his regime.
However, the benefits of taking out Saddam extend well beyond the borders of Iraq. Prior to the Iraq War, and thanks to a joint effort between Bush the Elder and Clinton, the world viewed American resolve through the filter of Mogadishu - and the tyrants believed that any American military action would be hamstrung by popular opposition once the body bags started coming back - and Clinton's subsequent tactics against Kosovo, namely bombing from high altitude to avoid casualties only buttressed that perception.
Now that America has shown that it will take out a despot that threatens our interests, not let the UN prevent us from action AND, most importantly, will maintain popular support in the face of casualties, all of a sudden the tyrants have to re-examine their premises that small-scale defensive actions would be sufficient to deter any American military action. And many of them are suddenly willing to cooperate with American demands - Qaddafi specifically alluded to the Iraq War and Saddams capture as the final determinant in his decision to end his WMD programs - programs that American intel underestimated.
So it is counterproductive to demand that we follow the same policy against Pakistan as we did against Iraq. Each country poses its own foreign policy challenges, its own ability to counter American power, and its own intertwining interests (with North Korea having the most, with ties to China and Russia and interested parties in South Korea and Japan). But now the despots eye the bloodied big stick in the hands of America and realize that their blood could be added to it as well. And that changes everything.