I would think there are several different considerations:
1) Indemnities to be paid
2) Costs of occupying troops
3) Damage/pillaging done by troops.*
4) Providing troops to serve in Napoleon's armies
5) Pay for French officials in territories under French administration - plus a French court in the case of Westphalia
6) Money taken for dotations held by French generals etc.
7) Loss of trade due to the Continental system
Import & export taxes - requirement to trade with France
9) Illegal extortions by the military.
10 Social/religious problems and offended national pride.
*How much damage was done by troops would presumably vary, not only with the disciplinary methods of the commander but also whether troops were in permanent occupation or in movement.
I daresay I've missed something, but that's quite enough to be going on with!