Paint jobs are cosmetic and you are not entitled to them by virtue of buying the game alone. You get everything you pay for with your $60, and ship skins are extra content that are not necessary for the game to function as advertised. They are vanity items and if you want them, you'll cough up the asking price, or you can't have them. It's that simple.
Are you entitled to them when you buy them from the store? Not sure what you're trying to say here. If it's "don't like it, don't buy it", then that's a little short sighted, don't you think?
Paint jobs and vanity items could be a great revenue stream for a game that otherwise has a finite income (other than new players and expansions). If the vanity items are enticing enough, players will buy them, and Frontier could do all kinds of things with extra income. As it is, there is currently little benefit to the player buying them so they buy less (if any), and the end result is Frontier have less revenue than they could have. I'd rather Frontier get all the money they deserve.