“People who design machines and airplanes {or buildings}, no matter how much they believe that what they do is good, the winds of time eventually turn them into tools of industrial civilization. They’re cursed dreams. Animation, too. Beautiful yet cursed dreams.”
― Hayao Miyazaki
I think the scenes of violence interspersed into the fairytale story did a lot of the legwork. It's also important to remember that Miyazaki's distributor employs censors and a lot of his films are very carefully walking the line to make anti-war films that get past the censors. Sometimes it's well done, like Nausicaa, Mononoke, or Howl, and sometimes it's more ambiguous like in The Wind Rises.