Bad Religion's logo is also known as the Crossbuster and represents a Christian cross with a red slash through it.
Greg Graffin: "(...) none of us ever regretted choosing that name or the logo. We consider the Crossbuster a kind of "no parking sing", in the sense that if you fly the logo it means "you won't find Christianity here." And the name and logo esteblished us from the beginning as a band that was willing to think for itself. It suggested that our songs would have a more philosophical edge. It kept us from having to deal with people who were unreasonably critical of music that challenges convention. In short, it gave us a freedom to do what we wanted."[1]
It was Brett who came up with the Crossbuster logo.
In 1989 Greg said "I wish it wasn't so offensive to people because other people could benefit from the ideas I think" but also said they chose it to piss a lot of people off.
References
^ Anarchy Evolution (2010)