1. Inefficacy of (Intercessory) Prayer
Studies have shown that intercessory prayer doesn’t work. The Bible says it does – Jesus says it does! – but it doesn’t. It doesn’t have better outcomes for sick people, or make you more likely to succeed in your goals, or anything! We’re supposed to be able to move mountains and be immune to snake venom, but people who truly believe they’re safe still die from Christian snake-charming.
Why would a God who exists and loves us and is all-powerful say that He’ll help us, and then turn out to not do anything at all?
What is your measurement for how God answers prayer? What timeline is your expectation? Where in the Bible does it say that all Christians everywhere will be safe playing with venomous snakes (which is putting the Lord God to the test, by the way, that which we are not to do)? When Paul was bitten by an asp, he was not playing with it, trying to "charm" it or trying to tempt God. Why do you believe that God is obligated to man?
2. Why sin/evil/etc? God can do anything, so why this?
Here’s the thing: this is not the best possible world, with or without Eve’s fruit of the knowledge of good and evil. If God is all powerful, why doesn’t He just make it so that whatever makes us have to go to Hell isn’t necessary in the first place? Not just believers: everyone.
God is just and righteous. He uses means to display His glory. God is also grace and mercy. If God used His power to have never allowed evil, He would never demonstrated His justice and righteousness and His grace, mercy and love would be absolutely meaningless. And if God saved everyone, then Jesus sacrifice on the cross was completely pointless.
A good God couldn’t possibly want all of those people to go to Hell, right?
Because God is good, He must hate and punish sin. Because God is good, that should be the most terrifying thing that anyone who is not in Christ will ever hear, because man is not good by any measure, in and of himself.
There’s the argument that God did exactly that through Jesus, but why? Why would he do that when Jesus’s resurrection happened 2,000 years ago (give or take), and we don’t have any solid evidence that the actual miracle of the resurrection (or any other miracles) happened?
Jesus perfectly demonstrated the justice, righteousness, grace and mercy of God through means.
And we do have solid evidence, you simply choose to reject it: more than 500 eye witnesses and the Bible, the most authentic document of ancient history.
I mean, if God is real, shouldn’t there be a lot more hard evidence?
You choose to blind yourself to the evidence that is all around you.
3. Dead Babies:
Everything that happens is God’s will, or can be made to fit His will, right? So how do dead babies make any [staff edit] sense? Babies don’t sin, and their lives aren’t object lessons.
This is called the Pelagian heresy, the denial that all mankind is born into sin. Babies are born with a sin nature. Your assumption is wrong.
4. Why doesn’t God communicate with us in ways that are more sensible and direct?
I mean, His presence is everywhere and all, but why doesn’t He find undeniable ways to show us that He is God? More of the clouds opening with a loud accompanying voice, less of the “communicating with us through our consciences” stuff.
He has through His inerrant and all sufficient word of the Bible.
I mean, His presence is supposed to be implicit, but it’s not. And even if it were – why couldn’t it be more obvious? Why would the subtlety even be necessry?
You are working from a false presupposition. God has made His presence known, you are choosing to suppress it.
Heaven is a big deal in the Bible. Miracles are a big deal in the Bible. But in my own life, and looking at scientific evidence and (not necessarily scientific) well-recorded data, there’s nothing that seems to indicate either one. Few modern-day miracle stories even do anything to prove YHWH, much less the resurrection.
Science is naturalistic and has no explanation for the supernatural. The are many modern day events that claim to be "miracles" that simply are not. However, the miracles described in the Bible are true, though you reject them.
5. Why are all of the arguments used to “prove” Christianity also used to prove basically every other religion?
You can apply them to Islam, to Buddhism, to Hinduism… it’s just the same kind of thinking, the same kind of excuses that don’t quite seem to work, over and over again.
This is simply a fallacious assertion, with no evidence to back it up. No other religion on earth shares the unique claims of Christianity. Not one. Islam, Buddhism and Hinduism have no Savior. Buddhism and Hinduism is Polytheistic. Islam is Deistic. To say that they have the same claims as Christianity demonstrates you have little concern for the truth or little knowledge of Christianity or those other religions.
If Christianity is true, and God is real and watching over us, and there is a heaven… why are we using the same logic, reasoning, excuses and cop-outs as everyone else is? Why do we need to?
The way humans use or abuse knowledge in no way nullifies the truth of God.
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If you truly have the doubts above and as you wrote, you think that they are rational, I am concerned that you have really not come to even begin to understand Christianity in the first place or if you ever were a Christian. However, it is possible to have doubts for the Christian, and if your questions are genuinely seeking the answers, it is good that you ask, but as you seek out answers, and if you do not see that those questions you pose are not refutable, I don't know that you are seeking truth.