The most popular reason seems to be these infant care seat covers come in a lot of "hip" designs and fabrics. Although come in a lot of styles and patterns (the has 33 styles, from Emerson to Spring Meadow), if you like to change the look or aren't happy with the one that you originally picked, a designer infant car seat cover can be a good idea.
Since they are removable, an infant car seat cover is supposedly easier to clean than the original car seat padding. Keep in mind that the padding/cover in most car seats is removable and washable in a washing machine too.
Pretty sure this is my favorite, especially if we go with a Minnie Mouse theme :) NollieCovers Infant Car Seat Replacement Cover Silver Package (Baby MiMi Mouse).
A more practical reason to have an infant car seat cover might be that they might help to keep your baby warm in the winter, so that you don't have to worry about keeping your baby in a . (It's been recommended that babies never wear coats in car seats.) Depending on the fabric, a thick, soft infant car seat cover can be like laying on a warm blanket.