The ball did hit the chalk line, but going over the bag in the air has nothing to do with it being fair or foul. If it is in the air, it has to HIT in fair territory for it to be a fair ball. It can be 10 feet fair passing by 3rd base but if it hooks foul after that and the first place it hits the ground is in foul territory then it is a foul ball. Now a ground ball that bounces before 1st or 3rd is a different story.
Therein is the key. A bouncing ball that goes over the bag and lands foul is fair, but a ball in flight that goes over the bag and does not then touch fair territory is, in fact, foul.