It seems like most commenters think the author is condemning Miyazaki for making propaganda, but what I just read feels more like a critique that this movie should have been darker and more challenging. IMO, while it sucks as a war movie, it is still is a morally challenging film about how innocent dreams can gradually and subtly become twisted due to a combination of the times, the environment, and one's actions. I agree that it's kind of odd how little of a stance the film seems to take against the evils at the time, but IMO, that makes it more powerful in how the movie leaves it up to the viewer to feel however you want to about it.
There are definitely moments in this film where you get to see a glimpse of the darkness underlining much of the movie - the first dream sequence where the bombs are dropped on Jiro in mid flight is a foreboding metaphor/warning that Jiro ignores, Caproni's cough-and-you-might-miss-it quip about how if given the choice, he'd rather live in a world with pyramids than one without (a statement that encapsulates a disturbing philosophy that there's nothing wrong with thousands of people suffering or dying to make something beautiful), the occasional glimpse of the secret police, etc. It's all very much from Jiro's perspective - even Caproni is just a sinister muse of Jiro's wearing a clever disguise - we only see what he experiences and thinks about.
I got the sense that Miyazaki was really probing the viewer to subconsciously look past all of the pretty art and cute whimsy he is primarily known for to ask themselves challenging moral questions about how atrocities can happen. To me it's a fitting way to tell a story that's about a man who only wanted to make something beautiful but had his mind so far into his own "dream" that he inadvertently decided that, like the pyramids, realizing it was more important than the thousands (or millions) of lives ruined or lost in the process.
All of this is extremely understated/ambiguous, which IMO is a good thing because it leads to articles like this one and lots of diverse viewpoints that often speak out in reaction to controversial films like this. I feel like this movie make more sense to me when viewed as Miyazaki's attempt at a much, much subtler version of a film like A Clockwork Orange, Kids, Lolita, etc. It's whimsical art and animation are unlike other Miyazaki films in how they seemed to be less designed to immerse the viewer into his beautiful imagination (although they definitely serve that purpose as well) and more about getting the viewer to look past aesthetic beauty to see something incredibly disturbing.