Red Rube first shows up in Archie's Zip Comics #39. He even gets the cover. His powers come from his dead ancestors. There's a heavy Captain Marvel influence on the story, all the way up to gagging the hero's boy identity so he can't say the magic words. There's no explanation for why the magic words would be "Hey Rube" other than that the kid's family name is Rueben (their spelling). As you know, the words were "used traditionally as a rallying cry among circus or carnival folk in a fight with townspeople" (Merriam-Webster). I didn't realize that (quoting Wikipedia here) "During World War II, 'Hey Rube!' was the open-microphone radio call issued by Combat Air Directors on American aircraft carriers to alert US Navy fighters to prepare to defend a task force from enemy air-attack."
I get the idea that MLJ's creators weren't very inventive. Most of their series' lead characters that I can remember, seem to have been clones of previously existing stars of DC, Fawcett, or other publishers more successful series.
"Rube" is a mild derogatory term for a farmer, country hick or bumpkin, used by the self-termed, sophisticated city slickers. As a term for unsophisticated, uneducated country folk, it was also used for rookies (first year players) in sports, coming from lower levels of their sport to a significantly higher league, because they didn't know "the lay of the land" (how things go in their new situation), while all the veterans knew all about it.
I guess that well-travelled circus folk thought they were "worldly", and thus, sophisticated, and all folk from small country towns were automatically hicks (who knew little about the outside World. I suppose "Hey Rube" could be used as a code term that The US Navy thought The Japanese and Germans wouldn't understand.