I don't know how long you've been an Atheist, so I don't know how much this may apply to you. Eventually you stop caring when people make that expression to you. You should because despite it contradicting your beliefs, most people who say it are genuinely saying it out of kindness and habit. Very rarely if they can pick up on your other beliefs will they try to be derisive and condescending to you. Very rarely. There are nasty people of all shapes, sizes, and beliefs so you shouldn't get hung up on that or let it bother you.
They've just become turn of phrases for me. I invoke God in a lot of sayings; and I've had other atheists question why I say it, when I don't believe in God. I forget God is actually something people believe in instead of just a word used in an expression. >_>