It's not about the price of the item. Most likely it is about prep time, and the interest in limiting basic dining to two courses. Desserts are cheaper to produce and prepare than appetizers. With two courses, they can turn the tables over faster. If you want three courses, you now have to pay extra - so Disney loses the faster table turnover, but they get more money for it. It's also not about what would make most customers happy. It's about cost efficiency for Disney. If you want the appetizers, you can still get them, you just need to pay more.
If they allowed a choice, there would be half the party ordering a dessert and the other half an appetizer, and they'd share.