Dustin Johnson was penalized for grounding his club in a bunker (a hazard) when the rules don't allow it. The standard penalty is 2 strokes and this penalty pushed him ot of the playoff so he wasn't disqualified.
What makes this situation unique is that the crowd was standing in the bunker and trampled it down beyond all recognition. Thus just like everyone else, Dustin assumed it was just a junky piece of turf.
The Committee has the authority to invoke rule 1-4 and in equity rule that under the circumstances this particular penalty would not apply. However, my guess is that since it is the PGA championship and run by the PGA, everyone was too busy patting themselves on the back over a great tournament and when the time came for a tough decision they were ill-prepared to make a good one. As expected, the stodgy always err on the conservative side which was unfortunate for Johnson.
When the rules don't align with common sense, there is a problem. In this case, the rules disappointed golf and cost Dustin Johnson dearly as well as robbing golf fans of what was lining up to be one of the greatest golf tournaments in recent history.