Atheist here. My personal philosophy says to leave them alone as long as they leave me alone. If you start to preach or force it on me, I'll do something in the range of: politely excuse myself, to tell you to fuck off, depending on how forceful, persistent, and annoying you are.
But in almost all such encounters so far I've just smiled and nodded because it was often coming from people using religion to bring them comfort in difficult times, and they were often not forceful. And if they say things like "God bless you", I take it as a sign of respect, because they often say it out of either gratitude or out of positive feelings towards me. I've been fortunate enough to not encounter many religious fanatics, though I've heard many stories of them and am ready to pull out the Ol' Reliable in the form of "Hail Satan" if it gets to that.