I also feel somewhat awkward praying in other people's houses, and for people who aren't heathen or my family members.

I obviously can't speak for everyone, but as an atheist I'm only uncomfortable/feel disrespected when people pray for my soul -- that I will find religion, kinda thing.

A Jewish friend of mine who was in Israel at the time of my mother's stroke told me that she prayed for us at the Western Wall, and I wasn't offended or upset at that in any way -- I was humbled, and grateful, and felt a lot of love for my friend that she would do that for us.