Had this happen to another umpire crew this past weekend.

[AtlUmpSteve]

To paraphrase what others have said:

The IFF rule is intended to protect the offense from a cheap double play due to runners that must stay at their base because the ball is obviously in flight and they would be doubled off if they run. With two or more such runners, it would be a fairly easy task by most players.

But nothing keeps that batter-runner from running, other than laziness or stupidity; there is certainly no jeopardy attached to the batter-runner running, like there is for the other runners. There is no reason to protect that person if he/she fails to run out their hit.