- They're bad at ruling
- They're aliens
Sure, the Han knew the Manchu were "different" and that they were being lorded over by an alien people. But for folks in the pre-modern age, that usually wasn't a big deal. Just think of the Normans in England, or the Mughals in India, or the Ostrogoths in Italy etc. etc.
The simple fact was, the Manchus were good rulers. The early Manchu Emperors were competent, hard working, and ambitious. They expanded the Chinese Empire far beyond its traditional borders, they respected Han Chinese culture (mostly) and, most importantly, they presided over a 2 century long economic boom in China.
During the Qing Dynasty, China's population doubled to 400 million. This was mostly due to more efficient management, infrastructural development and relative peace. A similar population explosion happened in Europe but that was mainly from technological advances in sanitation, and introduction of New World crops like potatoes and corn.
So... life was good under the Qing, no reason to complain. Chinese are simple people: keep us fed, keep us healthy, and let us make money.