It's one of the mysteries of the Bush administration. While they have reaped many of the disadvantages of talking tough, they have often balked when it comes to difficult decisions to actually go after al Qaeda, despite some risks of collateral damage. And so they let Zarqawi go before the war because of worries about allies. Now we know they may well have let Zawahiri go for similar reasons two years later. Musharraf seems to be an exception to the rule of "are you with us or with the terrorists." Money quote:
"The Special Operations guys are tearing their hair out at the highest levels," said a former Bush administration official with close ties to those troops. While they have not received good intelligence on the whereabouts of top Qaeda members recently, he said, they say they believe they have sometimes had useful information on lower-level figures.
Do we want to get al Qaeda's leadership or don't we?