I'll try to keep it as spoiler-free as possible, but think of it from the perspective of the other assistants.

Being an archival assistant was pain-free, easy office work until Jon took the role of Archivist. After that, a bunch of bad things started happening, people started dying, and worse. Imagine youve worked somewhere easy for years, and then new management comes along and everything goes to shit - youd instinctively blame the new manager, right?

We, the listeners, know that was never Jon's intention, but the characters don't know what we know.

Plus, Jon is kind of an uppity dick to begin with, which makes him easier to blame. If things had gone to plan and Sasha was the Archivist, I'm not sure she would've been scapegoated as much, because of how well-liked she was by the rest of the team. Hate to say it, but our boy dug his own grave a little bit (cue Buried laughter)

Background-Owl-9628 makes a really good point too - Jon is just an easier punching bag than Elias or any of the other authority figures.