I know that the Church is made up of fallible human beings

. However, one must still remember that the Catholic Church, being the Church founded by Christ, is still infallible in its doctrines and judgments, else we wouldn’t have anyone to go to in order to know the truth.
With respect to all the Jews who suffered, I believe the Church didn’t put all those restrictions on the Jews because it was antisemitic. There were Popes at those times who forbade Christians and if one does research one will immediately find that the Church did all it could to protect the Jews. The only Popes I see as being rather bad in their anti-semitism were Pope Innocent III AND Pope Pius V, the latter being alot worse than the former with him expelling the Jews from the Papal States. Where did they have to go? Then there was the case of Edgardo Mortara but, even though it was really, really harsh on the Pope’s part, the ‘kidnapping’ wasn’t meant for political reasons but to preserve the faith of one who was baptized. I wasn’t antisemitic, the same thing would have happened if the child was Muslim or Pagan (Edgardo even became a Priest and missionary and was successful at that).
Mind you, without shading over what these two Popes did, the Jews aren’t any better. I’m not talking so much of the atrocities and racism which they show not only to the Arabs but to the whole world (and by Jews, I mean those who actually do these bad things); what about the atrocities of the Old Testament? Those murders and wars which they performed on all those countries? The fall of Jericho comes to mind…

Sure God let them, but still, God is also our judge and without meaning to blaspheme, He can be pretty harsh (He punishes minor crimes like when He punished those children by setting bears on them just because they called His Prophet ‘baldy’).
Things certainly got better when the Blessed Virgin came around. There weren’t so many religious orders and so much good done by the Church than in the Marian age; it was the Marian age that gave us the greatest Popes and Saints. It isn’t because we moved on with the times, it was because we found out more about Her, we became more devoted to Her and we started to follow Her ways. We didn’t adapt, we Catholics followed Her. It all went downhill not only when we didn’t listen to Her message at Fatima, it all went downhill at the secular spirit of Vatican II. Vocations dropped, people became lukewarm, liturgical abuse, lack of Marian spirit, ecumenism, lack of the Marian spirit brought about by Ecumenism… it is only with Mary’s help that we can eradicate the poison of false ecumenism. We do not exterminate people of other religions because they disagree with us, neither do we slander them, but then again, neither do we support their beliefs or encourage them in the least to keep on with them. They don’t encourage us, neither shall we.
youtube.com/watch?v=hHDZ5rYiMz0&feature=related Couldn’t have said it better myself.