What happened is this: the NFL comp committee massively overreacted to Saints-Rams with this dog crap rule. The refs HATE the new rule. They hate the subjectivity of it, it's bad enough getting second guessed once on a play, they don't want it happening twice with a coach's challenge. Al Riveron has decided from on high that he and his guys are just not going to overrule calls or non-calls based on a coach's challenge for any play short of murder in the first. He wants to strangle the rule in its cradle and is trying to tell coaches - do not throw a flag and question us, we will not overturn. We don't care how obvious, we will not overturn.
So now we have the league telling players, coaches and fans that the rule is one thing, coaches trying to use the rule to their favor based on what the league has said, but Riveron and the refs going rogue and deciding that they are just not going to play ball.... which is what every one really wants at the end of the day (no reviewed PI), but also what everyone feels is extremely unfair and confusing while the rule is written and active as is.
So, great job NFL. Giving the people what they want. A-holes.