Complex sentence: They found support with Anglo-Irish Catholics, descendents of English Catholics who by the 17th century were reckoned to be "native Irish" and many of them were just as opposed to Protestant rule as the Gaelic Irish.
Split into simpler sentences: They found support with Anglo-Irish Catholics, descendents of English Catholics who by the 17th century considered themselves "native Irish". Many were just as opposed to Protestant rule as were the Gaelic Irish.