“why do so many people make a mezonos on pizza “
Is seems, at face value, that the Mechaber (siman 168) holds that only nuts, honey, etc baked with bread make it mezonot. Whereas bread baked with cheese or meat make it Hamotsi. We differentiate based on intent: dessert food vs dinner food.
But the Taz says that anything baked inside/on bread makes it Mezonot. According to the Taz, pizza is mezonot, unless one is Kove’a Se’uda. Therefore the only question is when is someone Kove’a Se’udat on mezonot.