Objections to NFL fines for unnecessary roughness fall into a couple categories.
Some objections pertain to the rules themselves. Others pertain to rules interpretations.
2012 Roughness Penalties: NFC West
Goldson struck Hernandez in the head area with his own helmet while Hernandez qualified for protection as a defenseless receiver. That's a penalty under the rules.
The 49ers incurred a 15-yard penalty for this particular play. They still came out ahead. The hit rocked Hernandez. On the next play, Hernanez failed to make an aggressive play for a ball, enabling an interception.
Safeties in particular walk a line on these types of plays. They want to dissuade opposing teams from throwing over the middle. They also want to keep their paychecks and avoid potential suspensions.
As the NFL continues to penalize players for hits to the head, we should expect defenders to adjust by lowering their target areas. Opponents could suffer fewer concussions, but taking hard hits to the ribs, back and abdomen is no fun, either.
In this case, Hernandez qualified as defenseless under the rule protecting "a receiver attempting to catch a pass, or who has completed a catch and has not had time to protect himself or has not clearly become a runner."
Goldson was flagged under rules prohibiting "forcibly hitting the defenseless player's head or neck area with the helmet, facemask, forearm or shoulder, regardless of whether the defensive player also uses his arms to tackle the defenseless player by encircling or grasping him."