Moon, there are many instances where runners have successfully made it to 3B on a ball hit in front of them. Mookie has done it at least a couple of times this year, with the reaction that he is such a smart baserunner. It's not an automatic 'don't run' situation. There are a lot of factors to consider, such as how hard the ball is hit and where the shortstop is playing.
It is sometimes a judgment call, and if a player is trying too hard, he might use poor judgment in that situation.