I've written quite a bit about how it is a mistake to equate "Christian" with moral goodness. This is still common practice in the United States, and it is a practice not limited to Christians. In fact, I hear it from other atheists more than I hear it from Christians. They are trying to call attention to hypocrisy but end up helping to perpetuate a myth.
When I encounter this assumption from Christians, it is usually quite blatant. I challenge it, pointing it out and explaining that I reject it. The version I hear from atheists is often more subtle. I try to make it more explicit since the person often doesn't realize what they are doing. I then challenge it and try to suggest alternatives. But why? Why do I bother with any of this?
My reasoning isn't complex. I bother because I view it as being harmful. It is harmful to atheists and other non-religious people. It is one of the main contributors to the bigotry we face. It is a barrier to equality. It is also harmful to non-Christian religious believers. It invalidates their religious traditions as "lesser than." This is not fair, as they have as much evidence for their gods as Christians do. I suspect it is also harmful to Christians, as we see with many other examples of privilege.
In the United States, this myth serves to maintain a religious class system. Christians sit at the top of the hierarchy. Below them, we find non-Christians who belong to other religious traditions. They believe in the wrong gods, making them morally suspect. But at least they believe in gods, so they've got that going for them. And then we find those of us who don't believe in any gods at the bottom. Pure evil.
The good news is that things are beginning to change. Voters have shown some willingness to elect officials who practice non-Christian religions. This would have been unthinkable not long ago. If attitudes toward atheists continue to improve, we could get there someday. We could have an elected official or two who identify themselves as atheists. Imagine that!
There are many good examples of harmful assumptions that go unexamined. Equating "Christian" with "good" is one of them. It doesn't hold up well to scrutiny. The problem is that it seems so familiar that we don't often question it. But we should question it. We should recognize how it can be harmful and work to dismantle it.