Having finally gotten through four seasons of Battlestar Galactica, I want to revisit the occupation/New Caprica storyline that was widely received as a criticism of the war in Iraq. The occupation arc is actually my favorite part of the series, not just because it was extraordinarily well done but because the rescue sequence, in which the Galactica executes a faster than light jump into New Caprica's atmosphere, releasing its fighters to they can take out the ground based defenses, is one of the coolest space opera battle scenes ever, hands down.
Jonah Goldberg's 2009 essay on the subject complains that the show devolves into liberal propaganda at this point in the series, although it should be noted that the objection is to the "liberal" part rather than the "propaganda" part. Goldberg is thrilled by an episode in which "saccharine liberal do-gooder" Laura Roslin, who becomes president of the colonies because she's the last cabinet member left alive after the Cylons destroy human civilization, revises her stance on abortion. Of course, Roslin does not do so because she decides life begins at conception or any other reason that reflects on our contemporary abortion debate, but because the universe is literally running out of humans. That twist is compelling because it portrays a character reversing a firmly held belief due to terrifying circumstances.
Similarly, the New Caprica arc, during which much of the crew of the Galactica is placed under occupation by the Cylons, is not a straightforward allegory where the United States are the Cylons and the colonists are al Qaeda. Quite the reverse actually--the point is to imagine what it would be like if America was occupied by al Qaeda, and in doing so force the audience to question their core beliefs by making them consider the morality of suicide bombing, by putting the practice in the hands of sympathetic characters rather than a bunch of Kaffiyeh-wearing Muslim stereotypes.
Goldberg laments that "the human suicide bombers are not young men brainwashed in a madrassa and promised eternal life with 72 virgins, nor are they threatened with the murder of their families—the tactics used by jihadists to create their human bombs." In other words, they're not Muslim-y enough. The objection is not that the series devolves into propaganda, but the wrong kind of propaganda.