Toby -
When I still had my German Shepherd, Piper, he was my flying buddy for a long time. He flew well, got really excited while taxiing, usually stood up and stared out the window. As soon as we took off, he'd get bored and just lay down and go to sleep.
HOWEVER, we had a scary situation in a Cessna 182, where the door popped open, he was in the backseat, and I got scared. I couldn't close the door (even though it was only cracked open a bit), so I reached back and grabbed Piper's collar and held him tight to keep him from checking out the new noise (lest he fall to his death, 6500 feet below).
The situation scared the crap out of him, probably mostly because of my actions. But as such, he never flew well again. He was scared to death, and would shake every time he got into an airplane.
I lost my flying buddy that day