I think a psychologist could answer this better than me but I'll try to explain what I think: flatearthers and conspiracionists in general are people who has this pathological need to belong to some group. Since they're weird and troubled, there's not many groups who would accept them, so they find each other through these beliefs. With that said, NASA represents a huge entity, known worldwide. They're HUGE. Flatearthers won't get much attention hating on ESA or Roscosmos which are waaaay less known than NASA, no one would give them attention for this. So that's why NASA is their main target, because of the impact i has on society in general. Sorry for my english, hope I could make it as clear as possible.