People put their hand there because your hand is a softer object than your goggles. If a paintball were to hit your goggles there is a higher chance of it breaking because of all the plastic. If a paintball were to hit your hand instead there is a higher chance it will bounce and you can keep playing.
In my experience it is a bad idea to put your hand in front of your face when running because it blocks out your view of what's happening on the field. A good player will see the field as they run, notice where everyone is going, where the incoming paint is being shot and adjust accordingly. Running to your bunker with your hand covering your face means that you can't see that player that just jumped into the snake or is coming to bunker you