Consider it a compliment (they do), say thank you, and move on.

In their mind, only a stupid, bad, misguided person would claim to be an "atheist"...and they think you are a good person, so you must just be mistaken.

Is it condescending? A little, but well-intentioned, which is a huge step in the right direction for the progressiveness of thought (versus hatred). These people need more "good people" who are atheist to come out of the closet to change that opinion...similar to how knowing more "good" gay or ethnic people can change other prejudiced opinions, indeed, it may be the only thing that truly does.

Similarly, when someone asks if you are "saved." Another compliment, they think you're nice, they wouldn't mind spending eternity in "heaven" with you (versus knee-jerk condemnation or damning you), so say thank you, appreciate their offer, kill them with kindness, and you both get to move on feeling better about the other side.

Black people had to deal with well-intentioned, but ignorant, people saying "I don't see color" for generations (and still do) until thoughts and opinions progressed, so I'm sure we can make do as well.