After the assassination (which lasts a fraction of a second), the plot turns into a police procedural following the investigation. The filmmakers seem to imply that it's a microcosm of the events leading up to the invasion of Iraq, after 9/11 -- basically the detectives and the Cheney administration are making the same mistake over again. The crime scene expert (one of the few officials in the film who aren't trying to burnish Bush's image, or cover their own errors), criticizes them for "reaching the conclusion and then trying to find the evidence". This results in an apparent wrongful conviction.
The Globe and Mail critic felt that a speculative movie about a sitting President was a fair subject. Whether a "Bush-like" president (just change the names slightly and insert actors' faces into the archival footage with CGI) would be as effective, could likely be argued either way.
http://www.theglobeandmail.com/servlet/story/RTGAM.20061027.wdoap27/BNStory/Entertainment/For the record, I thought that the way Bush was portrayed was actually quite sympathetic. And not many of the characters get that kind of favorable image (except the fingerprint expert and the son of the man who confesses, both of whom want to see the truth come out). The protesters seem unreasonable and clueless (e.g. the scene where some of them applaud after hearing the news, thinking it's a wild rumor) -- the investigators come across as biased and not entirely competent, and even the guy who is wrongfully convicted is shown to have made serious mistakes (trying to conceal his past).