Eh, I was just arguing to argue.
A very blithe pass at this would reduce it to:
American civilians use improvised weaponry to attack warship = patriotic goodness
Muslim civilians use improvised weaponry to attack warship = terrorism
But that's clearly a distortion of the context. For one thing, there was a declared war going on in the former case, and the American civilians seized the ship with the goal of hosing the British (or, to put it another way, stopping a threatened British attack, albeit one that the Americans had provoked) and then using it as a privateer.
In the latter case, there was no war, and the attack on the Cole wasn't to prevent an imminent action against the local populace, and the goal wasn't to seize and use the ship, but rather just to blow things up and make a twisted and violent statement. (And, arguably, to gauge America's reaction to this assault.)
So while the two incidents have some vague similarities, I would think it safe to say that O'Brien and company weren't terrorists. So back to my first statement at the top.