I try not to roll my eyes. Most of the time it is friends or associates trying to express that they hope I get through a hard time. So I swallow the eye roll. I know they mean well. But I think they also use it as a place holder to feel like they are doing something to help instead of going out of their way to think of something they could actually do to help. It is almost an automatic response. So I just ignore it.
It is more about them than me. So if they say they pray for me I just politely say: "Thanks." If it makes them happy, or they feel it helps, let them do whatever. Now, if they ask me to go down on my knees and pray with them, that's a totally different story.
I have friends that genuinely believe and dedicate much of their life to help others. I also have acquaintances that use faith as a weapon. If a genuine friend says this I thank them for caring, otherwise I say pray for whatever you want, I'm going to sacrifice a goat, specifically I'm ordering chiva tacos at my favorite Mexican restaurant.
It depends on context. It can be an expression of honest sympathy, but more often than not, the specific words "I'll pray for you" is the passive/aggressive Christian equivalent of "Fuck you". Ie; If I tell someone, "I'm going in for surgery tomorrow" and they say "I'll pray for you", I just say thanks. If they ask me if I believe in God, and I tell them I don't, that's the passive/aggressive Fuck you, to which I'll say something snappy.
My response to that most of the time is, thank you. I ignore the statement, "I will pray for you," I would rather just interpreted it, in my mind as I hope things get better for you. However, if they are saying after finding out I'm an atheist I will pray for you, I say, "Do what you will, nobody will stop you, but nobody is listening to you either."