The issues with applying ceramic coating mainly lie in the necessary time it takes to apply the product. To properly apply a ceramic coat, the car needs to be properly cleaned and prepared before the coating can be applied. It then needs to be applied by hand, which would increase the cost of labor and possibly time. From here, the curing process takes time that could be considered too valuable when mass-producing cars. All of these factors in combination could result in a raise in the cost of cars, and possibly a loss of sales. Alternatively, it could chip into the profits of the company given the extra costs involved.
With that said, manufacturers do use some types of clear coats that have similar (if less beneficial) effects. This includes basic scratch resistance and a lower chance of leaving water marks. But the benefits of having ceramic coating include hydrophobic effects such as resistance to rain, mud, and bird droppings. All on top of greater scratch resistance. While this makes it ideal for car enthusiasts and those who want to better protect their vehicle from damage, the added costs involved are too much for some manufacturers.