Firstly, this is an interesting, informative, thought provoking article.
Secondly, although propaganda can be scary, I do believe it can be less so if it is 1) open and upfront about the fact that is is propaganda, and 2) if the cause is good. Example: Casablanca - an absolute all-time classic - was originally conceived as war propaganda to get America to realise the war in Europe was something that required their urgent attention. And in the UK, we had films like Mrs Miniver and Went the Day Well? during the war - also both much loved classics, but also both designed as "good" propaganda (the former was genuinely moving and inspiring, and the latter an important warning about potential fifth columnists).
So yes - I'd argue not all propaganda is bad. But it is always important to be aware of it.
In the case of Marvel, I can definitely see the militaristic thread throughout much of it. It disturbs me to a point, but it is more subtle and less blatant than, say, Top Gun (another film made with full military cooperation). At least The Winter Soldier briefly touches on the traumas and difficulties faced by returning veterans. And Civil War (my favourite Marvel film) opens a genuine moral can of worms.