The pope (his handlers?) has made some very terrible judgements.
1. Unexcommunicating, and thus returning a holocaust denier to status of bishop.
2. Statements concerning homosexuality in the vatican.
3. Pressuring England and Ireland on not passing protections concerning homosexuals and women's rights.
4. Attempting to bring charges against an italian comedian who said that there is a special place in hell reserved for the pope.
5. Statements concerning condoms and africa.
and the list goes on.
I have zero respect for the pope. I think he is a horrible human being.
That being said, I have also donated to catholic based charities, such as Father Joe's Villages.
http://www.fatherjoesvillages.org/
There are certain catholic charties I wouldn't touch, and others I am quite happy to give money to.
for what it is worth, I am an atheist. I cannot judge these charities based on my views of Ratzinger, but based on the work that they do.