I think a lot of it has to do with the difficulty of explaining the character to a mainstream audience, especially why she wears an American flag if she comes from Themiscyra. Of all the explanations for that, the Golden Age version is the most convincing - the Nazis were clearly the bad guys, so it would make sense that if she came here to defeat them she would take on the imagery of their greatest enemy (okay, second greatest, but it would be hard to base an outfit on Russian winter). In our current world, it's harder to explain why an ambassador for peace would wear the U.S. flag, so it's easier to just refer back to her WWII origins.
It might also have to do with her origin story. Sure, Superman came into being during the Great Depression, but he wasn't sent to Earth to end it - the character just happened to appear during that time. Wonder Woman, on the other hand, originally left Paradise Island for the express purpose of fighting the Axis powers, so her existence has always been tied to a specific historical event. Reboots and retcons have done their part to change that, but it's still hard to completely separate it from the foundations of the character.
I'm not saying that any of these are good reasons to keep tying her to WWII, but those are the most likely ones that I can think of.
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