Whether it gets missed all the time has nothing to do with it. You're really arguing that even thought the ref saw it this time, he should have ignored it.
I'd agree with you if Tanner had gone down in the scrum initially for no gain/gain of a yard or two. At that point Smith had a handful of his guys jersey but he was in good blocking position and driving his guy towards the sideline, and if THAT had been called, it would have been ticky-tack. I think if that had happened, the ref wouldn't have made the call. Whatever was going on with Smith was minor and incidental to the play.
But when Tanner cut back and Smiths guy tried to break free, that's when it got more obvious/blatant. If the ref had kept it in his pocket at that point, he was ignoring an obvious hold that put one team in better field goal position, with under two minutes in a three point game. You're arguing that he should have ignored that. As a fan, I wished the ref wouldn't have seen it. But when he saw it, the hold was too important to the play and to the possible outcome to NOT call it. As a Cowboys fan, it pains me to say that, but he made the correct judgement call to throw the flag in that situation.