Communism gaining popularity is unlikely in the North American wasteland, not least because in the Fallout timeline self-proclaimed communists destroyed civilisation.
I think the bigger issue is that even 200 years later, people still hate the very idea of communism in fallout and would likely move against any self proclaimed communist settlement or movement.
As for why they still hate it, I'd say it's a 50/50 mix of leftover attitudes from the prewar USA, and Bethesda's heavy handed "hey guys, look, it's like 50s, but with ray guns robots? Get it, get that it was like the 50s?" style of "worldbuilding".
Also, I wasn't aware the mothership zeta aliens were communists.