Have you lost friends because you are an atheist? I have, and I suspect that this is not an uncommon experience. I've been fortunate in that most of the friends I've lost as a result of being an atheist were friends I probably would have lost anyway for other reasons (e.g., I moved far from where we used to live, they had children and I didn't, our interests and life experiences ended up moving far apart). There have really only been a few that I found hard to lose and genuinely regretted losing.
I know plenty of Christians who are not particularly serious about their faith. While they believe in gods, pray, attend church, participate in religious traditions, and so on, their lives do not center around their faith. For the most part, they seem to have little trouble with the fact that I'm an atheist. They tease me about it from time-to-time and indulge in some mild anti-atheist bigotry, but it doesn't typically cause problems. We seem to arrive at an implicit agreement where they do not discuss religion around me and I do not discuss religion (or atheism) around them.
The Christians with whom I have had problems are those whose faith does occupy a central part of their lives. Some have been unwilling to refrain from either trying to convert me or condemning me with their hell. They insist on injecting their religious beliefs into most conversations and become antagonistic in the process. Needless to say, this is off-putting. It puts me in the situation of feeling pressure to express my attitudes toward religion (because they repeatedly ask me to do so) and then being condemned for what I say. Maintaining friendships with this sort of Christian has not worked out terribly well, and a couple has told me directly that they are not interested in continuing a relationship with me unless I allow them to convert me.
There are many reasons two people who were once close friends might cease being friends that have little to do with atheism or religion. When I think back to some of my close friends in college, we were living in the same area, shared similar interests, and were having similar experiences. All these years later, none of this is necessarily the case. I moved across the country, our interests shifted in different directions, and we had very different experiences. I think that is often more than enough to end relationships because we reach the point where the only thing we have in common is some old memories. I have not been very successful sustaining relationships on that basis.
While there are undoubtedly some Christians who, like those I described above, become so focused on their faith that the notion of interacting with an atheist becomes intolerable, most of the time I've lost friendships over atheism it has been more about our lack of shared interests. As the other party becomes increasingly religious, we tend to have fewer and fewer shared interests. Conversation becomes more difficult because they want to talk about their faith, and I don't. We aren't sure what to do together. Much of their free time is spent in church-related activities, and it probably feels strange to them to hang out with someone outside that context. I can't blame either of us for this state of affairs, but that doesn't make it any less difficult.