Incidentally, the prosperity effect isn't caused directly by the spell, it is more of an indirect benefit (at least as the spell description alludes).
But to respond to you...
Prosperity, 99.9% of the time, affects all domains within the province equally - not just the province ruler. Landed regents do suffer from its effects more readily though (land regents are more directly tied to the land and people in a sense), but prosperity is a huge amalgamation of numerous factors all which points towards the general welfare and state of a province. Domain loyalty is also represented by the stability score. A negative score to stability often represents a domain that is going to go through some very difficult times.
From the regent guide:
All provinces also have a prosperity level, which is a measure of how well things are going in that province.
Prosperity is a catchall for the many factors that combine to make a province either effective or ineffective. It includes loyalty to the province ruler, but is also a measure of the general well-being of the province.
Prosperity is divided into a number of levels, each of which affects the ruler's ability to govern, collect taxes, and so forth. Prosperity is affected by taxation, wars, random event, and hostile or friendly manipulation (agitate domain actions for example).
Low prosperity means less income and an increase in action difficulty, while high prosperity leads to higher income and lower action difficulty.
Prosperity is applied differently depending on the type of action; often it will apply in equal measure to all domains taking action within the province, not just to the province ruler. For other actions prosperity only applies to the ruler and his allies (such as a state faith). However, in the case of domains that are openly hostile to the province ruler, the DM can rule that a low prosperity may actually aid actions taken against the province ruler or his allies, and vice versa.
Example: The Baron of Roesone has a very low prosperity in Caercas, meaning that the people are pretty dissatisfied. When his enemy, the Duke of Diemed, agitates against him, he actually gets a decrease in the DDC of his agitate action.