I'm an atheist. I've had believer friends ask if they could pray over me during a time when I was navigating difficulties. Do you know what I said? "I would be honored". Do you understand why? Because, while I don't share their belief system I recognize their request comes from only one place: love and caring. It would take a pedantic asshole to reject something coming from such a place. So, they did, and they felt better for it. And I did too. Good friends.
I am not necessarily critical of your comment. Just wanted to point out that not all atheists are militant fire breathing monsters. I do get upset when religion gets in the way of scientific truth and social justice (vaccines, gay rights, etc.). That said, in general terms, I am having trouble thinking of any believers in our group of family and friends whom I'd consider to be undesirable people. I would, without a doubt, be happy to receive a "I am praying for Jesus to make it better" card from any of them during trying times.