Exactly correct, I am a Bills fan living in NE and I can assure you they also think the NFL is out to get them. They can make a case too if you look at the whole deflate gate/sting the NFL did. They are the only team to lose two 1st round picks as penalties. I listen to NFL network on Sirius and this is a common theme, Steelers fans think the NFL is out to get them, Cowboys fan....like you said pretty much every fan base, the reasons are different. For Buffalo its small market, for NE its that Goodell hates Kraft, they all have their "reasons".
The reality is calls are subjective and the NFL officiating is inconsistent. Josh Allen getting called for a fumble against Minn while Mayfield gets an incomplete pass on the same play. Lots of inconsistencies........but I dont believe there is any conspiracy, nothing intentional.
Unconscious bias, sure we are all human. Screaming for calls works.... working the officials...some I am sure like some teams and dislike others, or more likely individuals...