Science -> Atheism? My Biggest Concern about Christianity

In general, scientists (even American scientists) are far less religious than the general public.  Why would that be?  Does science necessarily lead one to believe that the God of the Bible is a product of human imagination?

This is a delicate issue.  The best answer is: not necessarily but it is perfectly understandable why so many scientists don't believe in God.  You could reason that science is only good at explaining certain phenomena: evolution, mutations, chemical interactions, planetary motions, etc.  Science is not quite as effective in explaining how people behave, why we appreciate beauty in art, and what influences our worldviews.  Nevertheless, the power of science is undeniable and scientists are coming up with better scientific explanations of why we love, have ethics, and have aesthetic intuitions.

Now, I don't have an issue with other people believing in God.  People should be free to believe whatever they want as long as they do not end up hurting others, including themselves.  In fact, you can even think that atheists have no moral inhibitions because they are not scared of going to Hell and don't see Heaven as a reward.

My concern with Christianity is that it confuses some people's moral intuitions.  What in the world does gay marriage have to do with morality?  Or what about condom use?  Or pre-marital sex?  Or belief in God?  None of these issues directly concerns whether someone is doing good in the world.  All around the world, there are gay, condom-using, atheist bachelors who do charitable works and because I like this sentence I will end with it.

Note: I realize that many outstanding Christians are in favor of gay marriage, condom use, pre-marital sex, and have no issues with atheism.  At the same time, I personally know of some converts who actually developed moral concerns with the issues mentioned above as they became more devout.  I just wanted to mention this so that I am not oversimplifying the issue too much.