Bush could be Agent Smith though most people won't see the analogy Mr. Cole posits as it is a bit obscure. Then again I can't really think of a contemporary analogy that fits Bush well. Emperor Norton of San Francisco or Mad King Ludwig seem to be a better fit.
When I first read the Cole entry, I disagreed with the Bush-as-Smith analogy. Further pondering on the issue leads me to concur; Agent Smith initially is part of the system (both literally and metaphorically). However, his failure in stopping Neo leads him to go rogue, eliminating all previous compunctions (i.e. nation-building) and allowing him to take on new powers (i.e. Patriot Act). It's not perfect, but then again, no analogy is.
Still, Juan Cole makes a crucial mistake at the end of his entry in his assumption that Neo is the epitome of cool, and Agent Smith is simply a square:
If you are running for office, you want to be seen by the young people as like Neo, and not at all like Smith.
Speaking as a "young person" myself, a large part of the allure of The Matrix was that both parties (both the "free humans" and the agents) were incredibly similar in their abilities to dodge bullets, leap over gaps between tall buildings, and use automatic weapons with ease. The difference was in their goals; Neo and company wanted change, while the agents wished to maintain the status quo. Both sides were willing to risk everything in order to succeed.
Why, then, do we hate Agent Smith? Because he disgusts us. In the first movie, two interrogations take place; Agent Smith is present at both of them. In the first incident, he implants a bug (again, a symbol both literal and metaphoric) in Neo's stomach (causing him great pain) in order to gain information from him. In the second, Smith uses both physical and emotional abuse in order to gain information from Morpheus that would enable him to crush the rebels for once and for all.
My guess that the same people who bring up ticking-bomb scenarios whenever torture is mentioned would attempt to justify it if there was the possibility we could catch bin Laden if only we knew one crucial piece of information. That, however, is a argument for another post, as this one is quickly reaching its denouement:
Agent Smith is Abu Ghirab.