Andy suffered from severe amaxophobia the first month he was with us. Anytime we would walk towards the car he would pull back frantically on his leader trying to get away. He would vocalize intensely, as if he were screaming, "I can't go in there! If I go in there I'll die!". It was bad. One of us would have to physically pick him up and place him in the rear portion of the car (we have a small suv). Once in the car he would immediately lay down and start panting and drooling. At the time he was riding in a crate because he was small enough we were afraid he would get tossed around.
I don't know why Andy had such a negative reaction to the car and wonder if he associated it with a past bad experience (perhaps being abandoned at the humane society?) but because he would have to ride in the car relatively frequently we knew we had to retrain him post-haste. This took some time and tweaking.
In the beginning we simply tried talking to Andy in a reassuring voice anytime we approached the car and rewarded him with a small biscuit once he got inside. His discomfort and fear continued as he rode inside the crate in back so we eventually made the decision to move him to the middle section of the car and to let him ride outside the crate. We already had a car seat cover to protect the upholstery and the move gave him the reassurance of having constant visual contact with us up front.
It took another week of patient coaching to help Andy get over his phobia but it was well worth the effort. Now Andy is happy to hop up into the car on his own volition and rides quietly and comfortably wherever we go. He hasn't built up enough confidence to stand up and look out the windows but I'm sure that will come with time. It also helps that getting in the car usually means going someplace fun like the park or the pet supply store.