Once again, Germany was not a monolith, but a collection of independent states, and has to be judged historically that way. Very few of the minor states were pro-Prussian (such as the two Mecklenberg states), and Saxony had been forced to join Prussia in 1806, but was quickly turned into a French ally after Jena.
The major western and central German states initially forming the Confederation of the Rhine with Napoleon as ‘Protector.’ The treaty forming the Confederation gave troop totals for the common defense. France’s portion was 200,000. If you’re actually interested in the troop contribution of the German states, I’ll be happy to list them.
Napoleon generally left the internal affairs of the German states alone, with the exception of Berg and Westphalia, states that he had created out of the mess that had been the Holy Roman Empire. Both needed years of peace to consolidate and become a viable state, but unfortunately that didn’t happen.
The fact that both Austrian and Prussia had designs in the independent German states in order to dominate in Germany and gain more territory for themselves is the reason that the major German states in western and central Europe (Bavaria, Wurttemberg, Hesse-Darmstadt, Baden, and Saxony) became willing French allies. They retained their independence under Napoleon and were considered allies. Napoleon treated their soldiers the same way he treated his French soldiers, including the award of the Legion of Honor.
Westphalia is not the ‘standard’ or model for the states of the Confederation, and many of the ministers in Jerome’s government, as already mentioned elsewhere, were Germans, not French, and they served loyally and ably.
The Continental System did hurt the German states, but trade and industry developed in those states despite the economic problems.
French troops were quartered in the Confederation at the cost to the German states. But that was also offset by the troops spending their pay in those kingdoms which benefitted both local producers and merchants. There are always two sides to every story, and that has to be considered when remarking upon one side of any issue.