I would agree with the other posters....I think he may be uncomfortable in some way. My daughter has always slept well in the car, but a friend of mine has a son who would SCREAM and CRY constantly in the car. After a while, they figured out that he was a little too big for the infant seat AND they had neglected to remove some of the removable pad/pillows they come with as he had grown bigger. Poor guys was all scrunched in there. :)
I would try moving him to a convertible seat. My daughter is 15 months old and she really loves hers. If that doesn't help, then I think the poster who recommended motion sickness might be on to something there. Good luck!!