Atheist intolerance...?

Why are atheists always look down upon? I was at a friends house and we were about to eat dinner, They thanked god for the food and to live a happy life. So i just tried to fit in and i did too but after a while they asked me if i go to church and i said i was an atheist. I asked them and they said they were protestant Christian. They did not react in any way and are still nice to me and did not react but i was reading this article about atheism intolerance and they are just looked down upon by religious people. My friend's family like to help out but some other people are just always donating things and always miserable and complain about everything and it seems kinda sad and they are snooty and think they are perfect (Like my neighbors) and does being an atheist make you a bad person? How does believing god make you a better person? My neighbors complained to my dad about me getting an eyebrow piercing and said it was not moral (I am a guy) and all they do is complain how imperfect other people are and they always judge their religious views. I try my best to ignore it but even some people ask me what religion i am and i say i am an atheist and they get mad at me and told me that it wasn't necessary for me to disrespect her views! I mean come on, she was the one who asked? I do not judge believers but i judge the ones who judge me. Why are people so morally obsessed?