The simplest explanation is the both the most boring and the most likely: football decisionDoes anyone else find it surprising that we never heard anything about what happened with Malcolm Butler in the super bowl? I wouldn't expect BB to spill the beans of course. But, I do find it surprising that after all this time, no former player, no friend of MB, no former coach, no one - anywhere, ever leaked what was going on? Is that because only BB knows? That would seem a bit odd to me for two reasons, #1) is the Pats coaching situation so that no other coaches can ask a question and get an answer? It's an exaggeration, but could BB say "Brady is not starting this week" and no coach would ask for an explanation? I hope not. #2) Would MB not deserve at least some conversation as to why he wasn't playing?
IIRC, McCourty mentioned the squad captains on the defense were told there was a chance they may be without Butler. He was sick and may have missed some practice time. He hadn't been playing all that well and struggled in the AFCCG. Belichick tends to make these decisions in consultation with the coaches, so to the coaches it was just a decision that they owned together. Patricia pretty much said Butler wasn't part of the game plan. Bottom line it was a football decision, which is exactly how it was described by BB himself.
It would also explain why we've never heard anything, as there really is no story to hear. No-one really wants to revisit football decisions. The former players and coaches and Butler himself have all moved on.
It may come out some day long after his retirement that Belichick may feel the benching was a mistake. But we may be waiting a while.