By that logic, we ought to be OK with bombing of New York City since the 9-11 attacks happened there. The Shia Houthi rebels in Yemen that the Saudis are bombing had nothing to do with the Sunni al-Qaeda attack on the Cole.
It was the Yemeni government that thwarted any U.S. led investigation into the USS Cole. Our agents were intimidated, and were basically not allowed access to the attackers that had been apprehended. Clinton didn't fight for access, and the main suspects were allowed to escape prison. Plus Ali Abdullah Saleh who was the head of the Yemen government at the time, aligned himself with the Shia Houthi after he resigned as President. Saleh as President had been a target of the Houthi, but they kissed and made up, and he is now a behind-the-scenes leader of the group. So how do you know that there aren't any Cole attackers among them? They are obviously getting support from Iran.