I thought it was a nice dig at conspiracy theorists and how they manufacture these elaborate constructs that are just about justifying their own beliefs and have nothing to do with reality.
Although it kind of makes sense, in a way. Coulson has been a participant in most of the incidents that have revealed alien existence to humanity or brought aliens to Earth -- Thor's hammer, the Chitauri invasion, Malekith's attack (though only for the cleanup afterward), the whole Inhuman saga. Of course, that's just because he's an important member of SHIELD and it's their job to respond to such things. But I can see how Ivanov could mistake correlation for causation, given his existing fixation on Coulson. Gotta watch out for that confirmation bias.
And I don't think his anti-alien philosophy was random. In his first appearance, we saw that he's a traditionalist and is suspicious of anything new -- he scorns human enhancement and AIs like Aida as much as he does aliens. He hates aliens and Inhumans because they're a change from the baseline he's comfortable with, and he hates all such changes. So he already had reason to hate Coulson, and when he began to notice Coulson's association with other things he hated -- superhumans, aliens, advanced technologies -- it felt natural to him that the person he'd hated for so long must be the cause of all these other things he hated.