German Protestants and even German Jews received less prejudice and discrimination than did German Catholics. The discrimination against the Irish Catholics was based on their religion as well. Racially and culturally speaking, the Irish are not much different from the Welsh or Highland Scots. Yet Scottish and Welsh immigrants, almost all Protestant, assimilated quickly into American society. Rampant anti-Catholicism, stemming from the religious wars in Britain in the 16th and 17th Centuries, left a residual of deep, religiously based hatred of Catholics. Even the Jews (until the rise of "scientific racism" in the late 19th Century) did not suffer from the degree of prejudice inflicted on Catholics, irrespective of their national origin. Only the Mormons suffered worse in American history.
But the Gaelic Irish were more than just hated because they were Catholic--when they arrived in the 1840's, they were speaking Irish Gaelic only and illiterate, which made them nearly impossible to immediately assimilate into American society. Small wonder why the Gaelic Irish were victims of too many riots against them for many years, and lived the poorest parts of New York City and Boston (remember the movie Gangs of New York?).