Is he too warm or bundled up when he's in the car? Are the straps too tight or uncomfortable? Is there enough padding in the car seat? Perhaps something is digging into his back/legs, etc.? Is there something that makes him uncomfortable from a GI perspective; i.e., he gets a tummy ache, gas bubble, hernia (wild card but you never know)? etc., due to the position of the carseat? Have you talked with your pediatrician?
What is the scenario like when he's ok? When did your older son stop having this problem?
If not, could he just be bored? Perhaps putting some toys in his reach? Do you play kid music in the car?
Two of my kids HATED their carseats as well. With one I found there was a plastic thing underneath the padding that was making her uncomfortable - -I only found it once I took apart the carseat. The other one was too hot - - I ended up buying one of those snuggly fleece things that fit into the carseats and my son would be in a lightweight t-shirt and lightweight pants. These two children also had very bad acid reflux, preferred to be on their tummies (hated being in the upright carseat position, and it wasn't until they reached 7 mos. that things turned around and they were better.
I used to cringe when I had to put them in the car, but did my best, got through it, and they are fine now.
Hang in there!
J. - -mom of four