I think the two most obvious cases Patriots fans have against the NFL right now are:
1) It's clear there's been emphasis placed on Rob Gronkowski putting his hands on defenders to "help" get separation. It's clear this point of emphasis has gone way overboard, to the point that the guy can't be physical at all while on the field or he's getting flagged for illegal contact. This is, at times, happening when he clearly doesn't even use his hands at all, such as what you saw last night. As someone mentioned, this is the NFL directly trying to neuter the Patriots' offense, thus intentionally skewing the integrity of the game despite their repeated claims that they work to protect the integrity of the game.
2) It's also clear there's been emphasis placed on the Patriots' "rub" routes. From what I recall, we've been called far more often for OPI than any other team on those routes, despite the Broncos, Packers, Colts, and Chargers all running the same exact kind of routes with far less (or, to this point, no) calls against them. Again, this is the NFL directly trying to neuter the Patriots' offense, thus intentionally skewing the integrity of the game despite their repeated claims that they work to protect the integrity of the game.
If people can't see the correlation between what's being called on the field by the officials and what the NFL is clearly placing emphasis on that's directly solely at the Patriots, I don't know what else to tell them.
No one wants to sound like a baby by blaming the officials for a loss. That's not what any of us like to do here; SoSH isn't that kind of forum. I think we're all in agreement on that. But you can only turn a blind eye to what's happening on field for so long before you're willfully ignoring the fact that your trust in the league to actually promote and manage fair play is completely being taken advantage of.
Obviously, I, nor anybody else, thinks there was a memo issued saying "DO NOT LET THE PATRIOTS WIN THE SUPER BOWL! DO NOT LET THEM GO 16-0!" That type of thing would leak in exactly .02 seconds. But if you don't think the officials are being pressured to watch and scrutinize the Patriots closer than any other team - for no reason outside of post-Deflategate butthurtness - you're not reading between the lines whatsoever.