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)
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)