Chinese Emperors typically held very skeptical attitudes against monotheist religions as the belief of a supreme being that even surpassed the Emperor's holy self is considered "disloyal". There were cases in the late Ming period when Jesuit missionaries were expelled out of mainland China because of this reason, Alvarus de Semedo being an example. Overall, Ming Emperors tended to not care that much about religions though, because the impact missionaries had on the nation was so minuscule and the benefits they brought - much needed technology - outweighed any spiritual "disloyalty". This attitude was also shared by the Qing Emperors. The Jesuit scientist Johann Adam Schall von Bell was given the position of "Guang Lu Da Fu", a "Yi Ping" (First rank) title by Emperor Kang Xu, and this was despite the fact that Bell was a surrendered Ming official, and had helped Ming build cannons to combat Qing armies. So overall, it can be seen that the Emperors did not tend to have a very biased view on religions in general - it must be realized that the monotheist concept itself was quite novel for the Chinese at the time, so they did not really oppose it.

But enough about Christianity, your question is on Islam.

Even today, in China, Muslims are seen more as a separate ethnicity, instead of religious followers. This is because the majority of Muslims in China are - and were - of the Hui ethnicity, who live - and lived - in the Western province of Xinjiang. In fact, Islam was linked so much with the Hui, that any Han people who were Muslims would be called "Han Hui" during the Ming and Qing dynasty. So, for simplicity's sake, let's just observe the Hui people in general instead of the other Muslim minorities in China, as there were so few.

The Hui people were actually treated quite well as a minority people in the Ming Dynasty, to begin with. The Ming law code, as an effort to assimilate the minorities left behind by the Yuan Dynasty, forbade the minorities from marrying persons from the same ethnicity. The only exceptions were the Hui and the Kipchaks. Many Huis served in the Ming army, and in fact the Hui troops were very much needed for the "Three Campaigns of the Wanli Emperor", as two of the campaigns took place in areas with high Hui populations.

However nearing the end of the Ming Dynasty, the government took a more radical approach to Hui Muslims. This was as a result of the famines that occurred in China from the Little Ice Age: Hui communities living in the Shanxi province, along with Han peasants, actively rebelled against the government for imposing harsh taxes upon them even in times of bad harvest. Because of this, a new law forbade the Hui from possessing weapons and being congregated in large communities. Hui anger toward the Ming Dynasty culminated during the reign of the Youjian Emperor, and one of the most powerful peasant rebel warlords in China at the time, Ma Shouying, was a Hui Muslim - nicknamed "Old Hui Hui". But still, it should be noted that Huis were not specifically targeted by the Ming government and the Emperor in any way. In fact, Hui communities were some of the most ardent Ming loyalists during the invasion of the Jurchens. Thousands of Hui Muslims were killed as a result of a pro-Ming Hui uprising in Gansu in the late 1640s. So, it could be seen that, in terms of loyalty and treatment, the Hui must have been treated at least equivalently to the Hans by the Ming Emperor, otherwise they would not have been so die-hard loyal even after Emperor Youjian was killed.

In the Qing Dynasty, on the other hand, religious and ethnical tension was a real problem. This was evidently seen in the Panthay revolt, but in terms of the response from the Qing Emperors and officials, the attitudes were that of pacification and lenience, starkly contrasted with the treatment of the religious uprising of Taiping that occurred at the same time, not to mention cases such as the Boxer Rebellion. In all, Qing Emperors and officials seemed to regard Hui Muslims as a part of the Chinese society, much needed for the stabilization of non-central provinces. Christian converts, on the other hand, were seen as a threat with all the ongoing European "humiliation".