Dogs can't seem to resist the urge to stick their head out the window of a moving car, but allowing them to do so can lead to injuries. Dirt and debris can fly right into a dog's eye and cause serious damage.
The best idea is to crack the window enough for your pet to enjoy the sights and scents of the outside, but without their being able to face directly into the wind.
One other option is to outfit your dog with goggles specially made for canines (available at pet stores). They may look comical, but they keep the eyes safe.
Resources
Get more information on Doggles.