My dd did this too, and it was so stressful that I'd get anxiety attacks if I had to go out with her alone...I feel your pain!!
A few thoughts...my dd, as it turned out, had reflux, and the position she was in in the carseat was the absolute worst for her, I learned later. We reclined it a bit and she was a little better.
We also had a mirror/light/toy thingee that attached to the backseat right in front of her, kwim? She could see herself, and the thing played music and had lights on it. Toys might help too, they make such bright little things to hang from the bar.
Lastly, we'd put her in the carseat/carrier at "happy" times, (rested, fed and content times, not sleepy or hungry) I even gave her a bottle in it a few times. Sing to her, play itsy-bitsy spider, put her up on the counter while you cook or mix or whatever and just chat with her. It's important at those times to take her out while she is still happy, so she might change the assosciation.
HTH!