Steve White at Tapped sees in Transformers an apologia for militarism grounded in Michael Bay's close relationship with the defense-industrial complex. To which I say, eh. In purely ideological terms, Bay's oeuvre doesn't carry much of a message. The invasion of Cuba in Bay Boys II is egregious beyond belief but Transformers is, I think, basically sound.
Obviously, the film is soaked in enthusiasm for military hardware. On the other hand, the threat from the Deceptacons is quite real. Meanwhile, until the climactic battle with the Deceptacons, the tension in the film within the "good guy" camp. Mostly, the paranoia of the national security apparatus -- represented by the chief of Sector Seven and the guys who want to imprison Bumblebee -- versus the correct liberal view that we need to widen the circle of allies, distinguish between good and bad alien robots, etc. Similarly, the Autobots have a minor conflict between the more hawkish Ironhide and the more dovish Optimus Prime on the subject of killing humans, in which Optimus' more pacifistic stand gets a positive portrayal. All-in-all, I saw a balanced, patriotic, security conscious liberalism not the run-amok nationalism and militarism of the Bush-era GOP.
UPDATE: If you're interested, you might want to read a blog post on this subject from John Rogers, who has a story credit on the film in question, though I genuinely don't believe that the views of members of the creative team should be given special weight on these issues (he agrees with me, basically, but authorial intent is still irrelevant).
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