Unfortunately, this is one of those questions where the answer is "it varied." Older historiography, dominated by a Prussocentric narrative of German history, emphasized that the Napoleonic period was one of a heroic swell of German nationalism transcending the bounds of French captivity and subjugation. In this historiography, the boon of the Napoleonic interlude was it destroyed the vestiges of the Holy Roman Empire that prevented a cohesive German national state from coming into fruition. Historical research into German history in the last decades has significantly complicated this picture.

In general, the political elite would be of two minds towards both Napoleon and the Napoleonic regime within Germany (and it's important to bear in mind that for many Germans of this period, the two were often inseparable). The new Napoleonic empire offered the princes of so-called Third Germany a chance to elevate their station and autonomy within German lands. The growth and expansion of standing armies in the eighteenth century had put a great deal of stress upon these smaller German territories and the collective defense of the HRE Kreise was increasingly incapable of meeting the security needs of smaller states like Baden. If these lesser German princes acquiesced to the new Napoleonic order, the local boon to them could be quite rich. Both Württemberg's and Baden's territory increased significantly under the Rheinbund and brought in new revenue to their rulers. Napoleon also enhanced the social prestige of those German rulers who allied with him, elevating many to Kings or Grand-Dukes. Both the territories and the titles were things that these monarchs would not give up during the period of restoration and reaction. Furthermore, the expansion of these German states meant that they needed a new class of men to run them. Thus the Napoleonic interlude also witnessed an increasing professionalization of German bureaucracy and its nascent middle class.

Nevertheless, just because these elite benefited from Napoleonic rule it dies not follow that Germans saw Napoleon and his Rheinbund positively. Again, these attitudes varied quite markedly. Some German monarchs like Maximilian I Joseph of Bavaria or Frederick Augustus of Saxony found they could cobble together a functional working relationship with Napoleon. But this collaboration was not always received positively among governmental circles. Maximilian I Joseph's son and heir, Ludwig, actively despised his father's collaboration with the French. Other German elite had to deal with the French demands for taxes, conscription, and quartering on a local level and this obviously raised tensions.

On a lower level, there were few grassroots resistance movements against French rule. Although there are no clear public opinion polls, the demands of the Napoleonic empire, especially conscription, were largely unpopular in Germany, as they were in other parts of the empire including France. This disgruntlement seldom exploded into outright resistance and more frequently expressed itself in draft evasion or petty symbolic gestures like hanging out laundry when decrees celebrating French triumphs called for bunting.

The two big exceptions to lower-level German resistance to Napoleon were Prussia and Austria. The Prussian cavalry officer Ferdinand von Schill tried to raise a popular insurrection against Napoleonic rule in 1809. Schill's actions met with wide-spread support with Prussian military circles and there was a strong clique of anti-French sentiment amongst the Prussian elite than in other German states, so much so that Napoleon often tried to have these ministers removed. The Austrian Tyrol engaged in a guerrilla-style war against French forces in 1809, however adroit use of Bavarian forces and military pressure crushed this revolt. Nevertheless, both von Schill and Andreas Hofer (the leader of the Tyrol insurrection) became important symbols in both Prussia and Austria during 1813 for mass mobilization against Napoleon. It's important to note that the areas which reacted strongest against Napoleonic rule tended to be the states who lost the most territory and prestige from fighting and losing to the French. In many cases, French directives often dovetailed with the smaller German state's desire for centralization and increasing the power of the state.

The picture of a Romantic-based German nationalist uprising against Napoleon needs to be qualified. Certainly there were large numbers of German intellectuals who attacked French rule and its dictatorship. Friedrich Staps, a 17 year old self-styled German patriot tried to assassinate Napoleon in 1809. Beethoven famously erased his dedication to Napoleon in his Third Symphony. Despite these examples, intellectual resistance to Napoleon was more complex. Beethoven seriously considered accepting Jerome's offer to be the Kapellmeister of the Westphalian Kingdom. Other intellectual resistance to Napoleon became subject to a strong veneer of anti-Napoleonic propaganda during 1813 and became part of the official commemoration culture of the post-Napoleonic German states to cover up their long-standing collaboration with the French. Again, the strongest base of resistance tended to be in states that did not directly benefit from German rule, like Austria or Prussia.

The figure of Napoleon himself attracted the Romantics a great deal even if they were leery or repelled by the French political program. Napoleon often demanded the impossible and he sometimes got it, which is a core heroic principle of Romanticism. Although the figure of Napoleon became indelibly associated with French rule, Bismarck, born in 1815, liked to say he learned to hate France while suckling on his mother's breast, Napoleon's accomplishments were something that few intellectuals and monarchs could ignore. When Goethe met Napoleon in Erfurt in 1808, the former came away from the interview quite impressed. Although Napoleon tried very hard to have Goethe move to Paris, the latter refused, but the great poet never could bring himself to attack Napoleon because the Emperor was in many ways the embodiment of Romanticism's individualism.

Sources

Dwyer, Philip G. Napoleon and Europe. Harlow, England: Longman, 2001.

Forrest, Alan I., and Peter H. Wilson. The Bee and the Eagle: Napoleonic France and the End of the Holy Roman Empire, 1806. Basingstoke [England]: Palgrave Macmillan, 2009.

Laven, David, and Lucy Riall. Napoleon's Legacy Problems of Government in Restoration Europe. Oxford: Berg, 2000.

Mustafa, Sam A. The Long Ride of Major Von Schill: A Journey Through German History and Memory. Lanham: Rowman & Littlefield, 2008.

Rowe, Michael. From Reich to State: The Rhineland in the Revolutionary Age, 1780-1830. Cambridge: Cambridge University Press, 2003.

By German states, do you mean Prussia and Austria included or just the Confederation of the Rhine?