I got in a discussion on the BTRL forums with someone who simply could not see my equating the Colonials with Iraqi insurgents as anything more than hatred of the US. I've also found that people seem to get far more excited about that aspect of the episode than makes sense to me. Of course BSG is going to tie in with current events if it can, it makes sense from a ratings POV (many critics apparently mirrored the miniseries to 9/11, which seems like a bit farfetched to me, but I digress). And it makes sense from a viewership connection POV. If you throw something out there that's completely random, nobody will know what to do with it and it won't affect them one bit. But if you make it something that people care about, you suddenly get people interested.
EG the abortion episode was pretty clever, because they managed to pull it off without making it seem like it favored one side or the other. Of course, the brutal twist there is that Laura made the decision using Baltar's data, against her own morals. Then Baltar took Laura's internal position on the subject to publically assault her. Beautifully done, without necessarily favoring one side or the other, but either way you're forced to look at the decision from a different POV.
In the case of the New Caprica thing, it just makes sense to have the Colonials as the insurgents/resistance/whatever. If the Colonials had the definite high moral ground, it would just be good vs. evil. There would be no need for thought. The characters would have no dimension, no darker side that they needed to expose. But by throwing in the elements of Iraq from a different POV, BSG invokes the strong feelings on the subject and presents a side of it that the average American just doesn't see. Call it pessimism, cynicism, or whatever, but I feel that most people just don't do much thinking about it beyond the terrorists being "Them". "They" are out to get us. "They" don't respect our way of life. "They" are more ignorant and less rational than us. The episode turns this around and says - hey, there is another side to this. I think the reason that people don't want to equate the episode with Iraq is because in order to accept that comparison, they'd have to radically alter their opinions on who 'us' and 'they' are. They wouldn't be able to paint 'the terrorists' as quite the black-and-white enemy that makes them feel more secure about themselves. They'd rather be able to say "Well, they chose to attack us, that makes them a bad person."
I honestly don't know what RDM's motives are for portraying things the way that he did (Assuming that it was 100% his choice, of course). I can't refute the statement that he barely intended to mirror Iraq in any way, and the implication that it's all in our heads. However I do think that for something as charged as Iraq, nothing short of beating somebody on the head with the analogy (figuratively speaking) is gonna do anything. If it's subtle enough, people will just ignore it to preserve their way of thinking.
And of course I guess you could flip it around and say that the Cylons are the terrorists, this is what would happen if we let them win, but I feel that the metaphor of that is far more useful when somebody understands that it could apply to their own culture as well, because the situation is far more broad than just the current situation with Iraq, much of the stuff in BSG you could argue anywhere from a parent-child relationship to the clash of something as broad as Eastern and Western cultures.
