I've always read it as at least a little bit a comment on the Iraq war, but what's it's deal? It's the only anime I can think of that climaxes with a military coup, and its cool that mustang wants to put people on trial for war crimes, but then he gets in power and doesn't do it.
It's also just got a whole plotline about racism, but it feels slightly off? Like minorities are okay if they save your life.
One aspect I enjoyed was the presentation of a Fascist society from within that society. I think Triumph of the Will has so thoroughly made Fascism into this grand and serious thing when there were millions of Fascists who spent their days hanging out with their friends and having meals and making jokes. This predominant depiction of Nazis I think turns then into an alien force of things that look like humans but just goose-step and kill people (and the show utilizes that imagery when it depicts the Ishtvalan genocide).
That said, I think it undermines itself with the ending and turns Fascism back into an alien force imposed on humanity, but even then it shows how people can be easily taken in and corrupted by institutions and their propaganda.