This was not an isolated incident, although it does not equal to endorsement of the attacks themselves.

To understand these conflicting statements one must go back to the Civil War between Communists and Royalists after WW2. The former, after forming the backbone of a robust greek Resistance, hoped in establishing a communist regime. Unfortunately for them they miscalculated the aid USSR was prepared to give, after having agreed with the United Kingdom over the percentages of influence in the Balkans. The royalist government initially was backed by the UK but given the financial exhaustion of the British Empire, it was soon supplanted by the US. The american help during the Civil War formed the basis of a long lasting antipathy of the leftist Greece, which felt that they had been "robbed" of their rightful reward after having formed the majority of the resistance movement.

Still the Left never managed to win the majority of the population in post-WW2 Greece. A period of history which can be best described as a semi-democracy where the Communist Party was declared illegal and many thousands of communists were held in internal exile/prisons. This meant that the Right/Center viewed the USA positively, both for ideological reasons and the aid brought by the Marshall Plan.

In 1967 the dysfunctional democracy was overturned by a military coup which may have not been a US initiative but had complete support by the US. This cemented the hatred by the Left which saw direct US involvement against the struggle for democracy.

But the truly pivotal moment was the 1973 invasion of Cyprus by Turkey after a greek junta-backed attempted coup against the legitimate cypriot government. Even if the invasion could find some kind of justification, the occupation was and is still considered illegal by the totality of UN nation states. The US allegedly kept a pro-Turkish stance during the invasion but most importantly after the invasion kept a presumably neutral position which actually favored Turkey.

Eventually the junta collapsed under the Cyprus debacle but the effects of a perceived american "betrayal" right after having directly aided a dictatorship were were to last for decades. The Right felt betrayed by their benefactors, the Left felt vindicated for their hatred and soon afterwards in 1981 a patriotic, populistic socialist government emerged with anti-americanism a major part of its ideology.

Thus from 1973 to 2001 there was a whole generation which was raised to the feeling of betrayal by the US which was perceived as pro-Turkey, meddling in greek politics and of generally being highly hypocritical. This was of course adopted by the Left but was understandably uncontested by the Right, which did not see any allies in the US.

This was augmented by the bombing campaign against Serbia which was viewed as a fellow Christian Orthodox nation persecuted by the West. The greek media glossed over serbian belligerency which made the US look like as taking again sides favouring Muslims over Christians.

This feeling of victimhood was the main characteristic of anti-american sentiment, more so than the outright hatred of the US. This was obvious in 1999 President Clinton's visit to Greece, again after a quasi-war between Turkey and Greece where US neutrality was again viewed as indirect support of Turkish disputes of greek sovereign territory.

In the official dinner Clinton acknowledged that "When the junta took over in 1967 here, the United States allowed its interests in prosecuting the Cold War to prevail over its interests – I should say, its obligation – to support democracy, which was, after all, the cause for which we fought the Cold War. It is important that we acknowledge that". At the same time the greek President Stefanopoulos raged over Turkish aggression, the plight of the Greek-Cypriots and the streets outside raged over US-international aggression. Still, this short of apology won enormous praise which was quite indicative that while anti-american sentiment was deep rooted it was not going for blood.

This is why the attitude after 9/11 was more of sense that finally the US could taste some of its own medicine, rather than actual rejoicing like the pictures seen in many arab squares. There was no sense of identification with radical Muslim terrorists but more a hope that this act would bring some humility into the US. Of course the irony of demanding empathy by the US while professing none for what was the biggest US trauma after Vietnam, was lost. Still Greek payed nominal lip service to 9/11 and with the 2004 Olympic Games looming ahead went on to dismantle the vestiges of greek indigenous terror organizations and cooperating wholeheartedly on what Pr.Bush would call War on Terror.

tl;dr ? (Although I don't know if it is applicable in an Ask Historians thread :D) The US backed a semi-democracy after a Civil War which persecuted Leftists and ended up supporting a military junta. They were perceived as pro-Turkey in the Cyprus invasion and this led to an across political platform anti-Americanism. Importantly this never transformed into pro-USSR or pro-Muslim popular sentiment or state politics. 9/11 was viewed as a punishment for US hybris and not a national tragedy. Interestingly enough, anti-americanism has subsided drastically as the post-Junta generation slides into history.

source: the only book written on 9/11 and the greek response "Καλά να πάθουν, η ελληνική κοινή γνώμη μετά την 11η Σεπτεμβρίου" by Manolis Vassilakis

ps. I am not going into the israeli flag which is another issue