Bill Belichick doesn't just know more about football than the rest of us, he thinks about it more than the rest of us.
So the smartest guy in the sport doesn't just arrive at unpopular conclusions without a reason. Deep down, somewhere there's a reason he didn't play Malcolm Butler on defense in the Super Bowl against the Eagles. On a far less dire scale, he probably has some reason as to why the Patriots weren't in a big rush to work N'Keal Harry into the Patriots' offense after he came off IR.
We can take our guesses.