well I have friends who are atheist and I am a Christian, Yes it bothers me— but The only thing I can do for them is to understand. Everyone has life going through and through, and every decision we make was an impact of how life is treating us.
I know you had your reasons and I respect that. No need to push yourself further to please someone, And I'm proud of you for not being afraid. Some might not really agree with me, maybe a lot of christian would never. But This is my opinion about you— I love how you're choosing peace now.
I think compassion is what we need/ should show. Perhaps, one day your friend will find that one faith he/she could believe in but maybe they won't. I am sure at some point my friends were like that to me. While they don't agree with what I believed in at the time, they kept being my friend through thick and thin, regardless what I believed.
yes, It means that religion isn't really the problem. But the people itself.