If this creature has no +1/+1 counters on it (but is still on the battlefield because something else is raising its toughness), damage that would be dealt to it is still prevented.

If damage that would be dealt to this creature can't be prevented, the damage is dealt and a +1/+1 counter is removed from this creature.

If this creature would be dealt damage from multiple sources at the same time (say, because it's blocked by multiple creatures), all of the damage is prevented and only one +1/+1 counter is removed.