These were some of the most difficult questions that I encountered when I was doubting my belief in Jesus. I thought about them for quite a long time and despite the multitude of explanations I heard, I never found answers within Christianity that held any water.
1) Guidance of the Holy Spirit
The premise: Once you accept Jesus as your personal savior, the Holy Spirit (who is also God/Jesus) comes to live inside of you. The Spirit guides you and directs your heart. The Spirit reveals to you the true meaning of the Bible, God's living word, when you read it. Despite the fact that the Bible was written by fallible humans, you can trust that it is a perfect message from God, because the same Spirit who inspired the authors is dwelling in your heart and helps you to understand the meaning of their words.
The question: Why, then, are there so many groups of Christians who interpret the same Bible in such dramatically different ways? Shouldn't the Holy Spirit be the great unifier that easily clears up differences in interpretation, especially since that's supposed to be the mechanism at work which provides believers accurate information from the Bible despite its human authors and the difficulties of translation? How can it be that each group is convinced that they possess the true version of salvation, and that the other groups are heretics, based on the guidance of the same Holy Spirit?
An analogy: If Christianity is like Starbucks, the Holy Spirit is like the regulatory system that ensures that all of its stores are following the same recipes and creating a consistent product company-wide. You can go to any Starbucks in the world and they make the drinks the same way, because the employees have been clearly instructed on the protocol. If a human corporation can succeed at this, should not the divine speaker-of-hearts be even more capable of directing its members to the same One Truth? Yet there are endless divisions and contentions among the church, with each group believing that the Spirit is telling them their own understanding is the perfect truth and the others are disturbingly misled.
The answer that satisfied me: There is no unification of believers because the Holy Spirit does not in fact clarify scripture to those who read it. People confuse their own thoughts and beliefs with divine guidance. The Christian organism works just like you would expect it to work if you had a 1700 year old text that had been compiled and translated in different ways and understood independently by people of many different cultures and eras. The tenets of Christianity are just as varied as the people who believe in it, which points to it being a human creation and not a divine one.
2) Bondage to sin
The premise: The Bible says that the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, and self control. The works of the Flesh include adultery, uncleanness, lewdness, hatred, contentions, jealousies, outbursts of wrath, selfish ambitions, dissensions, envy, drunkenness, and the like. Humans, by default, are in bondage to sin from birth. They cannot overcome it. But with the saving power of Jesus and the indwelling of the Spirit, believers are liberated from sin, finally having the power to overcome any sinful pattern. Since they love God, they are motivated to avoid sinful actions which offend him -- and they have the power to do so.
The question: If all Christians possess the Spirit, and the Spirit is the only thing that has the power to change a person's actions from the works of the Flesh to the fruit of the Spirit, then shouldn't we see clear evidence of this reality in the lives of Christians compared to the rest of the world? Christians should be far and away the most loving, joyful, peaceful, kind people on the planet; and everyone else should be suffering a life of wretched sinfulness because they have no power to break away from it. This should be a clear and undeniable distinction. How do you explain the fact that Christians are just like every other group -- the most well-adjusted and healthy ones are happy, while the struggling and hurt ones are unhappy? The same is true of atheists, Buddhists, Muslims, anyone really. If the Holy Spirit is not the main determinant of who displays the Fruit of the Spirit, what is? Why do Christians remain trapped in fear, sin, and turmoil if they have been set free indeed?
An analogy: Imagine if someone taught you as a child that birds cannot fly by nature, but once they eat a specific kind of fish, they are suddenly able to fly and are not obligated to stay on the ground any longer. You grow up believing this explanation, but someday you realize that different birds have all kinds of different diets; that many non-fish-eating birds are flying, and many fish-eating birds are grounded. At this point would you not discard the dietary hypothesis and accept that what really determines a bird's ability to fly is its anatomical structure, weight, wing surface area, and the laws of physics?
The answer that satisfied me: Love, joy, peace, patience, etc. are not imparted upon human beings by the Holy Spirit. Those qualities are a part of our natural human capacity just as much as hatred, jealousy, and envy. Different qualities are cultivated in different people depending on a lot of factors, like the quality of your childhood, your mental and emotional health, and how strong and loving your community is. Exhibiting virtuous behavior has nothing to do with believing one set of ancient scriptures over another. These claims regarding the Holy Spirit's role in providing freedom from sin are a hoax. Anyone has the power to overcome destructive habits on their own, with the right understanding.
3) Creation of a broken world
The premise: God created the world according to the creation story told in Genesis. Humans were his crowning work, his children, the most beloved and significant of his creatures. He loved them and intended to live in harmony with them forever, without pain, suffering, or death. It was therefore to his great displeasure that Adam & Eve fell into sin after being tempted by Satan. Their nature was then sinful and all of their descendants would be born inherently sinful, and because sin is so reprehensible to God, they would have to be cleansed by symbolic sacrifices to be acceptable enough for his presence. The alternative, sadly, was to be sentenced to an eternity of separation from God, in Hell.
The question: Why did a loving God, who knows all things before they happen, create a world full of sin and suffering, and an eternal torment for unbelievers? Why did he allow the reality to be that only a small minority of humans who will ever exist on Earth will have access to heaven, and the rest will suffer eternally, if he loves all humans as his own children?
Maybe you've heard it's because humans had to have a choice to love him or not, otherwise it wouldn't be love. But why should that be the case? If God created love, surely he is not bound by some obligation to give humans the kind of choice that results in such chaos. He could have made the concept of love work in such a way that everyone is secure in it without needing to teeter on the edge of eternal punishment. If I can imagine that, so can God. And even if humans were to have the choice between loving him or not, why should choosing against God result in such a drastic punishment -- eternal damnation -- especially when many people on Earth never had the chance to learn about God in their brief lifespans, or were turned off to the idea of religion by very traumatic experiences which would cause our fallible minds to possibly reject God for reasons other than malicious rebellion?
Aren't there more likely explanations for the human condition other than the creation story -- that God made humans perfect but much to his chagrin a fallen angel turned into a serpent and tricked the humans away from God's perfect plan? How could he have allowed that to happen? Certainly he was aware of what Satan was doing as he did it. Certainly Adam and Eve were not the first beings to sin and rebel against God, if Lucifer already existed in his fallen state. If humans were to have any chance at a pure existence without sin, why would he allow his fallen minion to come in contact with them? If human nature was to be curious and drawn to the words of a tempter, why did God create them with that nature, instead of a nature where they would see deception for what it was and reject it? If they had refused Lucifer's attempt at corruption the first time, how many times would God have required them to be tempted? Just once, or every day until they succumbed? Then wasn't it his plan all along to end up with the miserable state of things we have now?
An analogy: I adopt a new puppy. I love this puppy, and I look forward to our companionship. I begin to train it to make good choices that will help it to stay safe and happy. But one day, I leave my puppy alone in the house, and on my way out I hold the door open to let in a rabid raccoon who is waiting outside. At the end of the day I return home and my puppy has been attacked and infected with rabies, and the raccoon fled out the window. Instead of using the power of medicine to do my best to heal the puppy and return to our original plan of a long happy existence together, I condemn it for being repulsive to me and I throw it out into the yard to suffer a protracted death, ignoring its cries of pain. Am I a good dog owner? Have I done what is fair? Is the dog to blame?
The answer that satisfied me: The creation story is a myth just like all the other creation stories that different primitive tribes believed in all around the world. It does not align with the idea that God the Creator is sovereign, benevolent, and all-knowing. It fits much more logically into the explanation that creation myths are human-invented stories to explain the origin of things they don't understand.
I never found good answers to these questions in Christianity. Maybe you haven't either (if you did, please tell me in the comments). How does that make you feel? Maybe your response is to say "God works in mysterious ways" or "we cannot fathom God with our logic, so your attempts to rationalize are invalid". If that is the case, how do you distinguish between something that is incomprehensible because it is so far above our level of consciousness, and something that is incomprehensible because it is a complete lie used to control you? If you aren't allowed to use your own human faculty of reason, your own instinct, logic, and senses, to determine what is true -- what do you have left? How do you know who to trust? If you'd grown up in Saudi Arabia or India, your same acceptance of religious authority would have undoubtedly turned you into a Muslim or a Hindu, and you would believe in it as adamantly as you do Christianity today.
If God is flawless and all-knowing, shouldn't the signature of his actions be that they are easy to understand -- because they are completely perfect, pure, and in tune with reality? Sick people are the ones who do confusing, chaotic, hurtful things. The actions of people who are intelligent, compassionate, and loving are the most easy to understand, because they have the ability to put themselves in your perspective and communicate in such a way that the important points come across clearly.
(You can find three more questions that killed my faith in this blog post.)