See e.g. http://time.com/3099950/china-muslim-hui-xinjiang-uighur-isl...
The TL;DR of it is that it has not much to do with religion specifically, and much to do with the region pushing for autonomy (which doesn't rate particularly high in the eyes of Beijing).
(This is not to say it's ok, just stating the reality of the situation)
The ordinary people's resentment towards Muslim stems from the Hui's abuse of political privileges to expand their religious strengths, such as Saria Law, to intervene Han people's daily life everywhere, from Ningxia, Gansu to Henan and Shandong, from Canteens, Schools to Police, Courts.
In the meanwhile, the majority has little to zero knowledge about the Uyghurs because only a few Uyghur people live outside Xinjiang.
The situation is really weird and there is a conspiracy theory saying that the CCP leadership has been controlled by the Hui Muslim.
BTW, the Hui Muslim and the Uyghur Muslim have been enemies since the Qing Dynasty.