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Why do quarterbacks do this? If they do this as a precaution in case there was no penalty, wouldn't they be flagged for intentional grounding?
Below is a link for intentional grounding as I understand it.
In high school football my coach told me to do it as a safety measure. Players on defense are trained to go after the ball and to be careful about touching the QB when he isn't in possession of the ball. Spiking the ball reinforces the notion that the play is dead. As a player you're very tuned into the sound of the ref's whistle. Most players stop immediately when they hear it, so the spike is for those who "didn't get the memo." Even at the high school level I've never seen a quarterback spike the ball in error after thinking a penalty was called when it really wasn't.
The QB either hears the referee's whistle, sees a flag thrown by an umpire or line judge, or any official waving his hands which are all indications the play is dead. At this point the QB realizes there will be no play. Pass rushers trying to sack the QB may or may not have heard or seen the same indications from the officials that the play is dead and may continue to rush the QB. Pass rushers are not in position to see as many officials as the QB and can be unaware the play is dead. As a protective measure by the QB to avoid getting knocked silly or driven into the ground, the QB will spike the ball into the ground. This should stop all pass rushers from hitting the QB. If they hit the QB at this point it is a dead ball foul and will result in a penalty to be assessed against the defense regardless of the initial infraction that stopped the play.
False start can't be called once a play is under way. It's usually called before the ball is snapped, or as you mentioned, while the quarterback is taking his drop back into the pocket. In this case, the quarterback will spike the ball because he know's what the penalty is (he can see the offensive line better than anyone), or just wants to do so, just because he can.
The only penalty that will prevent the play from developing (or continuing to go on) is a false start. That has to be called immediately when it's seen. In the case of offsides, the officials will throw the flag, but won't kill the play. This is referred to in the NFL as a "free play" for the offense, because if they do something bad (e.g. throw an interception) it will be nullified by the offsides call. Aaron Rodgers of the Packers is a master of this.
They aren't flagged for intentional grounding because after a referee blows a whistle for false start, the play is dead - anything that happens after (like the quarterback throwing the ball into the ground) doesn't matter.
