I do get a bit lonely sometimes, but that it has nothing to do with being an atheist. I don't have any really close relationships with someone that isn't also my family. I used to have lots of those, and I find myself feeling lonely when I reflect on that.
Even if the open windows of science at first make us shiver after the cozy indoor warmth of traditional humanizing myths, in the end the fresh air brings vigor, and the great spaces have a splendor of their own - Bertrand Russell