I think it’s more like “thank you for taking the time to think positively about my family.” Or in other words,“thanks for trying.” Religious or not, if a stranger is taking a moment to concentrate on the healing of your father, whether prayer is bullshit or not, that’s very kind.

I’m not especially religious, but I take “I’m praying for you” as less “I’m praying for a magical cure for cancer” than “I’m praying that you and your loved one will find peace somehow and you’re in my thoughts and in my heart.”