Ezra Klein objects to efforts at a politicized reading of Transformers on the grounds that "This is a movie about GIANT ROBOTS some of whom want to DESTROY THE EARTH" and therefore "may not, in fact, be a commentary on the righteousness of Operation Iraqi Freedom." This is, I think, naive and wrongheaded. It would be odd for a film like this to have been self-consciously conceived as a commentary on political events, but lots of films can nonetheless contain ideological content.
Indeed, it's the very shallow nature of Transformer's plotting that makes it so pregnant. The standard format for a not-very-original action movie pits a Hero against, of course, a Villain. But beyond the Villain, the Hero must also do battle with the Faceless Institution whose inability to grasp the true nature of the situation imperils the entire situation. This Institution comes in, roughly speaking, two guises. In some films, like Bad Boys, the Institution is portrayed as comprised of feckless bureaucrats who don't understand the Hero's need to Get Things Done. In other films, like Transformers, the Institution is portrayed as comprised of power-mad authoritarians who can't tell the good guys from the bad guys.
Now, of course, better, more sophisticated stories can have more nuanced ideological content (the Terminator films, for example, provide both a critique of the military industrial complex and a statement of the security dilemma), or else possibly none at all, or, perhaps, an ambiguous message (First Blood) that'll be read according to pre-existing prejudices. The key in all cases, though, is not to look for specific commentary on the passing tide of events (i.e., the SecDef in Transformers kinda looks like Don Rumsfeld) but for what broad values the film appeals to and endorses.