I agree with Tybee. Acknowledging them for what they are - a loving, caring demonstration of how they feel/felt about your mom.
Agree with all of the above - It's fairly easy for me to write a generic "thanks for support in a difficult time" or whatever fits the occasion. As a fellow atheist, I struggle with this more in person - "oh I'm sure your Mom is looking down and so happy to with....." I work to keep my face bland and simply smile and say "thanks so much for thinking of her" or whomever we're speaking of. This kind of personal dialog is why I was very glad both my parents were clear in their wishes to NOT have a funeral. Funerals don't seem appropriate places to debate theology, so when I have to attend, I do a lot of smiling and nodding and try to not critique things out loud. I find them very difficult, although I genuinely want to support those who are grieving. But people need what they need, and belief in an afterlife seems to be a big need for many people. Sometimes, honestly, I think my life would be a lot easier if belief were something that worked for me.