I do not know the answer to your question.
I would say that some are very prejudice, but many are not. For example, on the Moral Theology you will find very little on condemning homosexuals as such. In fact, almost everyone comes from the position of love the sinner, hate the sin.
As far as the Muslim thing. I think the reason is because many are scared. For example, cestusdei, who I see as one of the major criticizers of muslims was mugged and seems to blame the religion for the violence perpetrated against him. In the same way, many see the religion as the only tie between those who attack the United States, and so blame the religion.
However, you need to be careful, as you are doing the same thing. We need to be very careful when we paint with broad strokes, for we will surely condemn someone who is innocent. You are condemning all of Catholics and Christians of the actions of a few. I would say the vast majority, even on these boards are not prejudice, but rather prefer to just avoid the issues that are brought up. Part of this may be fear, as many people are accused of being “secret” muslims for defending islam. This should not happen, but it does.
Please do not label us all for the actions of a few.
A lone Raven