I just think it was the confluence of two corrupt influences.
Patriots were cheating. The NFL didn't know at the time.
The NFL wanted to control the narrative as it always does. Once the games restarted, the calls and win/loss record changed and the rookie QB just started...winning.
I don't necessarily think when the NFL started "helping" the Pats, that the goal was to "give" them a Super Bowl.
But, once they got in the playoffs... I woulda bet every last penny on them to win. There was no chance they weren't going to win. And has hard as I rooted for my Rams, I couldn't shake what I knew. Then the game started and everything I believed was on display.
So, I, personally, don't see it as some organized coherent conspiracy type thing.
I see it as various corruptions that coalesced into a much larger corruption. Essentially, the Patriots and the NFL were both cheating on behalf of the Patriots, each without the other's knowledge or benefit of that knowledge. The Pats for competitive advantage, the NFL because they sought to control and thus capitalize on the narrative as large corporations tend to do.
So, really, I just see it as two disparate rule breakers who both broke rules to benefit the same entity, but didn't know about the other. The end result was much bigger than either would have guessed.
I would agree in arguing against a grand conspiracy that the NFL sat down in a back room and decided that the Patriots should win the Super Bowl because...9/11. Firstly, they aren't organized enough to manage it. I mean...really. That part doesn't pass the smell test. These guys may know financials backwards and forwards, but they aren't exactly trained in spycraft... and if they were as discreet as they'd need to be to pull off something like this, then we wouldn't have all the OTHER incidents of mismanagement we have. So, really, that argues against the Grand conspiracy. I'm with ya on that.
That said... as @Boff097 has pointed out, it's a statistical anomaly that certain teams have more incorrect calls go in their favor than against them. I know over the last few years, my napkin math has about a 3 bad call to a 1.5 good call ratio for the Rams. I've watched almost every game in that span including two live games. In watching random league games. I've noticed promoted league matchups, the "marquee" teams are reversed, approx 1.5 bad calls to 3 good calls per game. Good calls being in their favor, not correctly called.
In the "Age of parity" when a drive can be killed by one penalty and with so many games decided by LESS than a touchdown, every game is extremely sensitive to refereeing.
We've seen it anecdotally as Rams fans, but there have also been a few studies that basically bear out that it's better to not be penalized, in general. That seems obvious, but the question was posed about whether the aggressive style that leads to more penalties was worth it. In general, the penalties were NOT worth it.
So, with institutional "points of emphasis" and bits of bias... like how guys on the various outlets are saying refs look at how much teams are penalized... and ref accordingly. Which is terribly biased. It means if a team was poorly officiated at some point and got a ton of flags, or played poorly and was flagged a bunch, that can become an institutional bias. That institutional bias can keep bad teams bad and keep good teams good. The removal of that bias, like Refs not wanting to throw a flag on a Patriot right after 9/11... can allow a mediocre team to win games it shouldn't win.
Which it did. Enough to get to and win the Super Bowl.