Unfair, but true...
Question: In my novel, I have a small yet powerful organization controlled by the main character. In many ways, they're a combination of paramilitary, secret police, and personal bodyguards; rather similar to how the Myrmidons (as portrayed in the film Troy, rather than mythology) were the personal following of Achilles. Anyway, they are fanatically loyal to the main character, who is a noble, though rather severe, person. The novel is in a more modern setting though, kind of like dieselpunk. My problem: Among a few lesser things, this organizations look could be compared to Nazis. Not fair, but true. They have no such ideology, and in fact they work towards good, but their looks are a bit similar. For example, their salute is similar to the Nazi salute; it's just that at the end of their arm, their hand is in a fist instead of flat. But this salute was based (ironically, like the Nazis') off the salutes of Ancient Rome, that's all. How can I portray these people the way I want, while fighting off these similarities to people like the SS? Thank you!
First, I think you demonstrate what their values are by their actions. Let the reader see what good they are working toward.
Second, I think the salute in itself demonstrates a militaristic, authoritarian structure. You do risk undermining the impression of these people as a force for good if you show them in this light.
Take any genre film you like where you have good guys versus bad guys and compare how each organization functions. I think you'll find that good guys tend to treat each other more like human beings with warmth, friendship, and humour while the bad guys tend to treat each other like cogs in a machine, with plenty of harsh punishment and threats. In the good organization, structure is less formal and salutes are rare because people are friends and colleagues rather than superiors and underlings.
I'm thinking of examples like Star Wars
(Rebels vs. Imperial troops), Buckaroo Banzai
(Blue Blazers vs. Lectroids), and Sky Captain and the World of Tomorrow
(Flying Legion vs. Totenkopf's robots).
I'm sure you can think of more and better examples.
So if you must have the salute, make sure you balance that with plenty of mutual respect and friendship. Let the reader see that it's better to be part of this team than the villain's team.