Sure, do it. Some atheists, especially self-identified "strong atheists," are offended by this sentence, but I don't mind it at all. I actually appreciate it, just like I appreciate when a believer says, "God be with you."
Why would I appreciate those phrases despite being an anti-religious atheist? Because these are often sincere expressions of good will on the believer's part. When a Muslim tells me that they hope Allah helps me with something, or they wish that Allah "guides" me to the right path, I take little to no offense because these prayers actually represent the epitome of what the average Muslim considers to be good and desirable. They are not wishing me harm; they are wishing me the very best thing according to their beliefs.
So, by all means, pray for me if you would like. I'm not going to mind it. Quite the contrary, actually; I tend to appreciate it when it is done with sincerity.
Why would I appreciate those phrases despite being an anti-religious atheist? Because these are often sincere expressions of good will on the believer's part. When a Muslim tells me that they hope Allah helps me with something, or they wish that Allah "guides" me to the right path, I take little to no offense because these prayers actually represent the epitome of what the average Muslim considers to be good and desirable. They are not wishing me harm; they are wishing me the very best thing according to their beliefs.
So, by all means, pray for me if you would like. I'm not going to mind it. Quite the contrary, actually; I tend to appreciate it when it is done with sincerity.