I disagree- any holy war instigated and fought in the name of religion looks bad for that religion... unless being judgemental and not turning the other cheek are called for by that religion. Which unfortunately for every Christian is not the case.
Its not one thing, or even a few... its all of the points you mention plus so much more.
Why do bad things happen to good people? The suffering question might be an existential one that we all have to deal with, but it kinda answers itself for the atheist, don't you think? I've never believed in any gods that I can recall and have never really had a problem with that question, either. It sucks that suffering happens, but it does.
The Christian 'why' is a pitiful attempt, IMO, and does nothing to make me want to believe in a higher power.