When I was an agnostic, I used to be offended when Christian family and friends told me they were praying for me, because I thought (correctly) that they were trying to convert me. I took it as them saying: I don’t like you the way you are, therefore I will pray to a God you don’t believe in so that you will be different.
It’s apparent from this thread that unbelievers react in different ways and not everyone is bothered by it, but some are, so my advice is to be tactful. You can always pray for someone without telling them that you are doing so. If there is a specific issue, for instance, they are sick or going through a difficult time, I think it’s fine to tell them you’re praying for them to get better, since they will see it as your way of saying that you care about their health and well-being, rather than as a subtle pressure on them to convert.