There certainly is terrorism from the Uyghurs. Whether you want to call it "Islamic fundamentalist" or "separatist" terrorism doesn't really matter. The terrorists themselves call it "Islamic", which has ended up tainting the Hui by association in the minds of the Chinese. But you'll note that all the Western coverage of repressive practices complains about how steps are being taken specifically against the Uyghurs, who are the group making trouble. The government seems perfectly capable of distinguishing unassimilated Uyghurs from assimilated Hui, much more so than the general run of Chinese.

The Chinese government doesn't really go for publicizing terrorist attacks. We could learn from them, in that regard.