Well, air moves into your lungs due to a pressure gradient created by the expansion of the lungs (increase of volume). In other words, when the diaphragm allows the lungs to expand, the pressure in the lungs is less than the pressure outside the body, which is why air moves into the lungs. Air flows from high pressure to low pressure. The pressure associated with moving air is less than that in still air (Bernoulli's principle). So maybe the pressure gradient between moving air the lungs is significantly less than it is with still air, resulting in it being harder to breath when you stick you head outside a moving vehicle.