Those are implied apologies from the embassy for the actions of the makers of the film, to the protesters.
To protestors; not to attackers. The embassy statement came before the attacks. It was an attempt to quell an imminent threat. And frankly, the embassy was right to do so. The film that stirred up the protests was so blatantly offensive and downright evil that an apology - not an implied one, but a full one - was warranted on behalf of the American people. That's not saying the embassy deserved to be attacked, but the statement wasn't made after the attack, now was it?
Something to consider: Most Muslims in the Middle East come from a culture where speech is officially approved by a totalitarian or theocratic figure; it is not free. Most Muslims in the Middle East, by virtue of their being poor as dirt, are also often uneducated and ignorant of American values with regard to free speech. Is it any wonder that they think these films and statements made to offend were approved by the government of the United States?
On another note, and to respond to this thread in general, no, I think Romney's foreign policy credentials are shot at this point. He flubbed Britain, he flubbed Israel, he flubbed Russia, and now he's flubbed the Middle East. This man is a walking foreign policy disaster, far worse than Bush the Younger. This will very likely nudge independents even further into Obama's arms, but not by much - as others said, this election is about the economy, not foreign policy. If this were 2004, Romney wouldn't have a chance. (Not that he has much of a chance regardless.)