Many of my problems with Christianity are inherent to the religion, and not a reflection of the actions of its followers.
I have a problem with the concept that disobedience to any entity, no matter which specific entity it is, must always necessarily constitute a sin. There is nothing wrong with seeking knowledge, but Genesis tells us it is wrong when God says so. Sometimes the noblest act is defiance of a powerful authority, rather than submission.
I have a problem with the tendency of all gods in all religions to draw a line in the sand and state, "Beyond here, no mortal shall trespass." This is illustrated in the story of the Tower of Babel, wherein God reminds the puny mortals of their role as his inferiors. This is the sort of thing that retards scientific progress, such as stem cell research or cloning, or causes people to fight back against it, such as the HPV vaccine, based on the apparent assumption that some problems are just not meant to be solved.
I have a problem with the scapegoating found throughout all Christianity, from the original sin passed down to me because a snake convinced a rib woman to eat a fruit, to Jesus being sacrificed for the times I've lied, to God's specification in the Third Commandment that he will punish your great-grandchildren if you reject him. My "sins" are my own, I don't want anyone else taking that responsibility from me, and I refuse responsibility for anyone else's sins.
I have a problem with the concept of infinite punishment for finite crimes. There is no crime I can imagine that warrants eternal torture. When lack of belief, or belief in another god, is held as one of the crimes most obviously deserving this punishment, it is illustrative of a flaw in the system. Even under the interpretation of Hell as simple separation from God (which, in my experience, hasn't been so bad), the suggestion that there can be no redemption after death for disbelief in the face of an overwhelming lack of evidence is fundamentally unethical.
I have a problem with the free pass given to God for atrocities either committed or commanded. The mass murder of children is never justified - certainly not because their Pharoah refused God's authority. This kind of story encourages a tolerance for "collateral damage" that should be obviously vile. The many justifications trotted out by apologists for these crimes are insufficient defense, and I would be happy to debate the specifics with anyone who cares to challenge this assertion.
I have a problem with lauding unthinking obedience to any authority figure as a virtue. Abraham nearly sacrificed his son on God's word. The only thing that separates him from the many "God told me to do it" convicts we see murdering their children, or innocent bystanders, or whoever, is that God stopped him at the last second. But what if the word never came? No, the correct answer was, "No, Lord, I will not murder my son for you. And if this disobedience invokes your wrath, then let it be on my head alone." Unquestioning obedience to orders is not a virtue; it is a short route to atrocity.
I have a problem with human sacrifice. If you buy into the apologetics that she wasn't sacrificed, but only delivered into the clergy for the rest of her life (I don't), I have a problem with the assumption that uninvolved parties are obligated to someone else's agreement with God.
I have a serious, serious problem with teaching that the end of the world is soon, unavoidable, and generally a good thing. Modern technology has brought the ability to end the world closer to the reach of vastly more people than ever before. All it requires, today, is a fanatic with access to the right buttons. The availability of those buttons is likely to only increase - the world's populace simply [i]must[/i] learn that the apocalypse is to be averted, not sought. This is why the USA is trying so hard to stop Iran from obtaining nuclear weapons. And yes, it's a Christian problem, too.
I have a problem with the concept that being human is inherently bad - so bad that we deserve to die just because of the fact that we were born human. This is a central concept to all Christianity. The reason Jesus had to be killed was to save us from a horrible fate that we entirely deserve. It is because God is "just" that he could not simply forgive these apparent failings, and required a blood sacrifice to appease him. This is how cults behave - they tell you that you are worthless, that you deserve only pity at best, but then they "save" you. This is manipulative. This is evil. And it's a core part of Christianity.
I could go on. Do I lay these failings at the feet of Christians? Not usually, no. Most Christians/Jews I know tend to gloss over these and other problems with their scripture. Most Christians seem to agree that the Ten Commandments form the foundation of American law and tradition, despite the fact that the First and Second Commandments are in direct violation of the First Amendment.
It sounds great to say that religions basically just teach you to be good to other people, but only by ignoring the vast majority of any given religion's scriptures could you come to that conclusion. Humanism, however, does actually teach you to be good to other people, and nothing more. This has nothing to do with why I believe religions are not true, but it does address some of the reasons I'm glad that they aren't true. I am not one of those who wishes he could believe, or who believes religion is just a set of stories that help us be more moral. The Bible teaches submission, either to God, fate, or ignorance. I reject it, thoroughly.