Of all the world's philosophies, none are so contradictory as atheism. Atheism's greatest weaknesses are reason and morality. A common attack on the Bible is its alleged immorality. Atheists find a verse they don't like and call it evil, then conclude that, therefore, the Bible is not true.
There are so many things wrong with this line of reasoning that whenever I write about it, I never actually know where to start or how to structure it. But really, all the flaws have the same core: Man wants to be God. See, the thing about moral laws is that there must be an agent to give them. How can one obey a law that does not exist? Think of a speed limit. Where does a speed limit come from? To whom are you accountable if you break it? A law needs a government. But in atheism, there is no divine government. If atheism is true, "that action is evil" is no more authoritative than "that ice cream flavor is disgusting".
Thus, every time an atheist accuses God of evil, they are referring to their own opinion. That is to say, atheists ultimately claim "in my opinion, God is evil, therefore in my opinion, God does not exist." Are you convinced yet? Neither am I.
So now we move on to the fact that not only is an atheist's opinion not authoritative, it is also inconsistent. Every attack atheists levy against God, they have a view similar to the one they ascribe to Him. Take, for example, infanticide. Atheists love to claim that God kills children, occasionally pointing to the flood as an excellent example. How many babies died in the flood?
First, we can answer "we don't know". The Bible says all flesh had corrupted its way (Genesis 6:12). The Bible tells us that God is slow to anger (Psalm 103:8). The Bible tells us that God waits for iniquity to reach its completion before He runs out of patience and judges a nation (Genesis 15:16). I could go on, but the long and short of it is that the human race was so evil, it's impossible to know if even one baby actually died in the flood.
But let's assume they did. Let's imagine the human race wasn't quite so corrupt as to sacrifice their own children for their own prosperity. First, let's point out that this would make them better than modern secular culture. In the modern world, it is entirely permissible to slaughter children. Not only permissible, it is celebrated. And many atheists chant "Abortion sends babies to God faster!" to try to shut up Christian Pro-Lifers who protest this abomination.
But furthermore, there is some truth to the statement. To murder a child is wrong, not because I think so, not because any human or group of humans say so, but because God is the author of life. It is His right to give life, it is His right to take life. If He wants to call children back to Himself, He has that right.
And that's the point. If God is the author of life, God has the sole right to dictate what is moral, and therefore what right have we to judge Him? Can our plates rebel if we decide to smash one? No! The only time it is wrong for us to smash a plate is when we are not the owner of that plate. Similarly, it is always permissible for God to kill a human, because He is always the owner of humans.
This, in itself, is a failure of atheism: They think of death the wrong way. An atheist believes if a human dies (which, let's face it, is inevitable anyway), they are destroyed completely. But a Christian knows that when anyone dies, their body alone is destroyed, but the soul (the thing that makes you you) remains, and goes into God's presence. In other words, in the very rare occasions when the author of life commanded people to kill, He was actually saying "send them to me", and when He takes a life, He isn't ending that individual, He is calling them to Himself. For final judgement.
Now, for a baby, that's not really a bad thing. Children are ignorant, and therefore innocent. Had God allowed them to grow, they too would have fallen into sin, likely copying, and even doubling the evils of their fathers, but through the flood, God spared them that.
But the ultimate problem is what happened to the adults who did evil and faced judgement? This is the main problem atheists have. See, each and every one of us is born with the law of God written on our hearts (Romans 2:12-16). Through this, we not only obey the law by nature, we also know how much we fail to obey it. We all know that we're sinners. So really, when an atheist reads about God's judgments against sin, they're reading God's judgments against themselves. It is this that they hate, and indeed they are supposed to hate it.
But this hatred is not designed to make us hate God, the Just Judge, for justly judging us. Rather, it is supposed to drive us towards Him in repentance. See, God has two natural aspects. He loves justice, but He loves mercy. God doesn't want to punish sinners. And so what He did instead was send His Son, Jesus, to live as a man, and despite knowing no sin Himself, He took the wrath of God for sin. In other words, the judgment that should have been levied upon us was instead levied upon Him. Thus, through faith in His death and resurrection, we can be forgiven. There's no point trying to judge God, He'll win that war every time. Not a single atheist, on Judgment Day, will even have the guts to so much as whisper their objections under their breath. Instead, accept the grace that was freely extended to you. That's the only logical option. What criminal, offered a reprieve, will instead turn and criticise the law for the previous criminals executed under it? Repent, you fools! There is no sense in being a martyr for injustice.