If God or religion is an important aspect of your life or you have creative offerings on these subjects then you most certainly should write about these concepts.  Freedom of speech is a beautiful thing and I believe that every writer should embrace this gift and be willing to tackle inflammatory topics within their work. 

Life is such that you will always find somebody that doesn't like what you wrote or  has a different perspective on the topic.  Those facts don't mean that you have written the wrong subject matter, it is merely a statement of our individuality as people.  To write about God or religion may evoke controversy and you would have to remain courageous in your supporting your work.  Part of being a writer is rejection, whether from peers, editors, publishers, or society.  To write highly charged subject matter means you just have to develop a thick skin and get that message out there.

The only time I could see writing about God and religion as wrong is if what you write is a form of hate literature.  If you wrote a piece of work that expressed hatred toward a certain population, then not only is that wrong but it is punishable by law.

If you have some to write about God or religion be bold and go for it.  And someone doesn't appreciate your views then it is really their problem, not something you did wrong.