In the pilot episode we find that Cylon spines light up during sex. But we also find out that you can't distinguish Cylons and humans despite the peanut bulbs in their vertebrae! It was undeniable from the first that the Cylons were not characters in any rational sense.
The suicide bombings; the United Flight 93 allegory in "33" the explicit threat that the hijacked prison ship posed (by being crashed in a suicide attack a la 9/11); the use of subversion instead of straightforward military attacks (no Islamic government has attacked the US since the days of the Barbary pirates, if I remember correctly); the emphasis on the religious motivation; the monotheism (orthodox Muslims hold that Trinitarianism, the predominant Christian theology, as well as some doctrines about Mary are equivalent to polytheism); Colonial society is portrayed as a secular one---not even the priestess was devoted to a particular god or goddess in this supposedly polytheistic society!---making the Colonials effectively religiously pluralistic, i.e., "free" and "democratic," just like US; the absolute refusal to countenance any discussion of any motive for the attacks other than innate and uncaused malignity: All these things indicate that the Cylons were essentially Muslims in a 9/11 series.
There is no clear divide between religious and racial bigotry. The anti-Semitic tradition in the majority Christianity appears to be the reason all Muslims are so commonly equated only to Arabs, and anti-Semtism is notoriously both racial and religious (and when Jews are identified as Communist plutocrats, politically conservative.) If you don't see any equation of Cylons with Muslims, I suppose that you won't be offended by the new BSG (although its writing flaws offer cause for boredom.) However, it is really hard to understand how it can be unacceptable for someone to be offended by the series when they do so that equation.
Even by the end, when the blatant magical thinking has taken over rational plotting, the Hand of God pushing the corpse to annihilate the Cylons expresses the His judgment on the Cylons=Muslims. It was never in the cards that the supposed realism of the series would result in humanity's mere escape, much less its annihilation. As a 9/11 series, it had to end in the defeat of the Cylons=Muslims, and as such, the guilt-free wish fulfillment is having God do it Himself. (But we got to daydream a little about doing it ourselves, heh heh.)
Again, if the 9/11 aspect went over your head, I'm sure that the series was just badly/weirdly written. Again, considering how judgmental people can be about mere bad writing, refusing to accept that people can reject a show for racism is really bizarre. The new BSG was however highly praised for its topical relevance. Indeed, only that and the hot chicks/hot sex were ever singled out for praise. For many people I think it's the 9/11 aspect that gives the otherwise rather drab yet pompous tone of the show a weight that made it tolerable.
To slap the "It's a 9/11 Parallel" label on it, IMHO, is just catering to folks who don't know any better and actually believe 9/11 was the worst and ultimate event, ever, and I gotta believe Ron Moore is far too intelligent/knowledgeable to be in the camp that believes that.
Yes, the premises of the show incorporated a wildly right-wing view of current events, which safely limited every pretense of neutrality and even-handedness and openness to dissenting opinion. But it has nothing to do with intelligence or knowledge, it has to do with moral integrity, and I have no reason to rate Moore's integrity very highly. And by the way, the Abu Ghraib episode was "Flesh and Bone." Since this turned out to be an episode about a Cylon psychologically torturing sweet Starbuck while feeling no pain itself
we have an excellent example of how reactionary the show's take on current events really was. Everybody knew that stuff worse than Abu Ghraib was going on before the pictures surfaced and most either didn't care or even approved. The scandal was that the pictures meant people had to talk about it. The new BSG offered a bunch of BS as its contribution to the so-called debate.