When you hit the gas pedal in a car, you get pressed backwards in the seat. That's physics. So why does a helium balloon dart forward, into the acceleration? Is helium immune to physics?
The secret to understanding why the balloon moves this way is looking at why it flies in the fist place. Helium balloons are filled with a substance that is less dense than air (or at least less dense than air at ground level). Gravity pulls everything down, including the helium and the air, but some molecules are more adept at getting to the ground than others. The helium molecules are getting shoved out of the way by heavier air molecules, and so they are forced upwards. It's the same thing that happens when your salad dressing separates out and all the oil is on top. The oil molecules are resting on top of denser molecules. Put a little balloon around that oil, and it would have exactly the same behavior as a helium balloon.
When you're in the car, it's not just the objects in the car that continue to go forward after you brake, it's the air as well. All that dense air is rushing forward and muscling the helium balloon back, making it seem to move the exact opposite way of everything else in the car. Try it out sometime!