My opinion only.
Because for some people, it's confusing that one does not believe in God, or Gods in general. For those of faith, it is impossible to fathom how someone could not believe in the God that they have faith in. So they could either be threatened by it, or ask those people about it.
Asking questions about something that confuses you is an intelligent way of doing things - that way you will learn about that which you don't understand, and therefore not fear it anymore.
Lack of understanding is the root of most hatred - people fear what they don't understand, and for some, this turns into hatred/anger against those who confuse them
I'm fine with all the questions - I like the fact that people are willing to ask and broaden their horizons. I know that most of those of faith will not change to be atheist based on an answer I give - but I don't want that anyway - atheism is what works for me, and faith is what works for them.
I ask my own questions of those of faith, as I seek to understand more about their religion, and am thankful that people will answer those queries.
I guess for those of faith - nothing could be more perplexing than someone who cannot believe in the best thing that they've come across in their lives. I dunno.