I think cry it out implies that you are expecting your child to cry through something...hunger, saddness, wanting mama.... A child crying in a car seat is totally different. It took me a while to get to this place, but if my dd was well fed, clean diaper, had toys, and was just unhappy about the car seat I had to stop pulling over every 2 miles because she didn't like the seat. I put her favorite tunes on, I talked to her (and really, more to me) to tell her that she was okay, mama was right here, and that I know she doesn't like the car seat but she is in the safest place possible when we are in a moving car.
It started to feel really unsafe to always be pulling over and holding her on busy roads/parkinglots. It always ended the same; no matter how long I held her she always started crying as soon as I put her back in.
That being said, I didn't leave her to cry just cause. I have to leave the house....we can't just be home all the time...Someone has to go shopping, kwim?
Basically, she didn't like the car seat and she wanted me to hold her. I spend all day and night holding my sweet daughter but it just isn't safe to do that in a car. I had to help her learn that by making her car seat as fun as its ever going to be....good music, toys, me talking.
We went though a phase of this and she is just fine. She sometimes is unhappy there, but as soon as her favorite music is on, shes happy! I guess that's my suggestion. Get some good Dan Zanes CD's...you will all be happier with some singing. I am sure when she is 18 I am going to miss the days when I could comfort her by singing polly wolly doodle at the top of my lungs!!
Good luck mama!!