I've actually heard this from Christian's before. They're tiny brains couldn't comprehend how I could be a good person, how are you so nice? All of that despite being a non-believer. I can't count the number of times I've had to explain that a book of fairy tales shouldn't be the reason for life decisions.
Yeah, it's pretty ridiculous. But like the other commenter said when you've been indoctrinated from an early age and socialized to think that everyone without "god" is a shitty person (when honestly the reverse is typically the case), you tend to approach all interactions with "unbelievers" thinking that your (fake) niceness is going to convert them or draw them in. HUGE EYEROLL
And with them being insulated in their religious bubbles, they cannot fathom how people they are told are "inherently evil/wicked" are actually normal and pretty nice people. The irony is my observations and experiences lead me to conclude that religion makes for shitty human beings and I've become a much kinder, and genuinely empathetic person by shedding it.
If all you've ever been told is that atheists are evil demonic entities, and you can be seen as a doer of kindnesses ... of course that's cognitive dissonance for a believer whose head is filled with such idiotic notions of what atheism is and atheists are like.