I think it's primarily because, as Jesus said, "They will hate you because of me." People hate God, they hate people in general, or they hate something in their life, and they turn this hostility toward Christians, who are no better or worse than anybody else.

Of course people are disappointed with the church. They are also disappointed with capitalism, or America, or their jobs, or their parents, or whatever. Nothing is perfect. But disappointment with the church seems to translate readily into hatred of all Christians.