DD used to be the same. I sometimes put a bamboo muslin in the seat before her to act like a liner because I can't think the synthetic materials that the seat must be lined with help much.
I think that's a good idea, the muslin wraps are a cooler fabric or even a cooler cotton, you could grab an offcut from spotlight or something. I find our car seat is really warm too! We put covers on the windows and have just turned bub around facing th front which has helped heaps as the air con can acutally reach him now.