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.
The main reason I always connect it to Iraq is the timing, the series started in 2003 so it's just right there.
I get that, but it just doesn't add up quite right. Iraq wasn't a US colony before invasion, but germany did hold colonies wherein they committed genocides to maintain their power and access resources.