How often do you take him out in the car? When we got Alfie I was advised to take him out in the car at least once every day if that's an option, right from 8 weeks, to get him used to it as soon as possible.
I'd recommend that you take Fergus out in the car as often as you can, even just for short trips. Make it a matter of fact, "this is what we do" thing, with as little fuss as possible.
How do you react when he whines in the car? The advice I read here (and which I followed!) was ignore him when he whines, and praise him when he is quiet, ie not to give him any attention at all when he whines. I took Alfie with me every day as I gave my daughter a lift to school, and, at the start, Alfie would whine for the first 5 minutes, but within a few days he wasn't making a peep.