I don't think there's some sort of conspiracy going on. Every team gets nailed with bullshit calls at one point or another.
I don't even blame the refs to be honest. The root cause is the rules, they're fucking terrible. Imagine being a ref on that play knowing full well that the league essentially doesn't want quarterbacks to be hit at all and being told to enforce those shit rules. If you want to get paid and stick around for a while you're going to "do your job." It's exactly the same thing when it comes to cops busting people over some bullshit, the laws are the problem (for the most part), not the cops themselves.
Digging deeper, here's what I think is the major problem that will never be fixed: Intent needs to be the deciding factor in whether a play was intentional in harm or not and/or on rules they are heavily emphasizing nowadays. But this will never happen for two reasons: 1) It would slow the game down because they'd have to review a shit ton more plays (assuming they decided to make it reviewable only by the officials ala scoring plays and turnovers), and 2) It'd be too difficult for them to make that judgement call while the play is happening (for the most part), I just don't think they'd be able to do it.