Saying that most Christians are good people poses no problem for the atheist.
As an atheist, there is no reason why I can't agree that most Christians are good people. Most Christians I have met in my life have been kind, trustworthy, honorable individuals who treat others as they would like to be treated. They have been my family, intimate partners, close friends, bosses, co-workers, neighbors, and so on. These Christians do their best to live productive lives, and many are genuinely concerned about the plight of their neighbors. Even though they may hold some beliefs I find strange, many care deeply about improving the world in which they live.
Of course, everything I just said applies equally to atheists and persons who are believers in other religious traditions. Most atheists are good people. Most Jews are good people. You get the idea. Most people are good people, regardless of which religious tradition (or lack thereof) they accept.
Saying that most atheists are good people poses a problem for the Christian.
Unfortunately, the Christian cannot seem to agree that most atheists are good people without adding an important qualifier, at least implicitly. The qualifier is comparative in nature, placing Christians on a pedestal above non-Christians. The atheist may be a decent person, but he/she cannot possibly be as good as the Christian. The atheist or the person from a different religion may be good in some respects, but he/she is still going to hell to be punished for all eternity. The Christian bible is quite clear that those of us who do not believe in the Christian god are not equivalent to those who do in many ways. Their fate in the afterlife will be very different from ours.
This is an example of what I mean when I say that religion is inherently divisive. Believers in any religious tradition are indoctrinated to believe that theirs is the one true faith, and that means that everybody else is necessarily wrong. Their god beats all others. Their morality trumps all others. Their fellow believers are more worthy, deserving, etc. than everyone else. As an atheist, I am not encumbered with this particular prejudice (although I am certainly susceptible to many others).
Claims about most Christians being good people have little relevance to the larger question about the costs of religion.
What some Christians fail to grasp is that claims involving how most Christians are good people have little relevance to the larger question about the dark side of religion. Religion does not make people good (or bad). It may at times inspire people to do great things; it may at times bring out the worst sort of atrocities and foster irrationality. As Steven Weinberg reminds us:
(Religion) With or without it you would have good people doing good things and evil people doing evil things. But for good people to do evil things, that takes religion.To understand why this is the case, one simply needs to consider the earlier point about religion being inherently divisive. If I am taught to believe that people who do not share my beliefs are inferior, there is little to stop me from treating them accordingly. If I am indoctrinated from birth to believe that persons with different beliefs are morally inferior, condemned to hell, diabolical, etc., the door to atrocities opens wide. If this indoctrination has also diminished my ability to apply reason by convincing me that faith is superior, look out.