Depending on the manufacturer of the car seat cushion, the cushion itself and the fabric cover can be waterproof. However, you should understand that majority of the cushion used in these devices are composed of foam of varying densities. Foam is a porous material and is water-absorbent, not waterproof. The only time the cushion can be considered waterproof is when it is encased in a waterproof or water-resistant liner or casing.
As for the fabric cover, many of these are removable and can be cleaned in your washing machine. If they are made of synthetic materials where the individual fibers are packed tightly together, then you can have a waterproof fabric cover. However, if the fabric was only treated with some chemical, it may only be water-resistant.