What side are you on?
I think most people believe that they, their thoughts and their feelings are more than just a chemical reaction. They have a belief that there is more to themselves than the material. This is why it is so easy to subscribe to the first religion we are exposed to -- it gives us an initial framework for our thoughts. Eventually we may mature intellectually and become aware of other ways of believing and become aware of inconsistencies our own religion or way of thinking. What happens after that varies and depends somewhat on the persons circumstances. Although the decision that is made is rarely rational we come up with apparently rational reasons to support our transition or lack thereof.
If a person has made a huge personal investment in their belief system, or if their job or social well being is strongly connected to that belief system, making a transition is hard. A person who is a pastor or an evolutionary biologist might have a harder time making a transition than, say, a truck driver. Some others make a slow transition away from their belief system while others might reject every aspect of their belief system and overshoot into something else just as irrational. I don’t think it matters a lot where a person ends up provided that their belief system doesn’t cause harm. I think it is also important that there be tolerance for other people’s beliefs and respect for the people that adhere to them.
Within every belief system you have ideologues and fanatics. These are the people that usually cause harm and that view people with other belief systems suspiciously. They are eager to assume that their ideological opponents are stupid, disingenuous, liars and even evil. Religious ideologues are often rightly criticized for this sort of bigotry but it is hardly restricted to religion. You can also find this bigotry among some atheists, political partisans and cultural adherents as well.
In my opinion what is important is not so much what you believe, but what side you are on. Are you on the side a tolerance, respect and peace or the side of bigotry, hate and even war?