Uighurs are persecuted for the same reason the CCP tries to destroy the Tibetan ethnic group.
Both these groups have strong independence movements that want to break away from China.
For the Tibet case, a great book about the history of China-Tibet relations and the role the British played in it is "The Snow Lion and the Dragon", free to read online: https://publishing.cdlib.org/ucpressebooks/view?docId=ft2199...
For the Xinjiang/Uighur case, I don't have a book recommendation. Uighurs are a Turkic people, so they don't really fit into China culturally. Xinjiang became Chinese about a millennium ago, but Uighurs continue to fight for an independent "East Turkistan". The movement's headquarter is in Munich, afaik.