One of the most interesting things to come across while reading secular, atheist, and anti-theist viewpoints is when there is a blatant misunderstanding about the thing that they are scrutinizing. This is incredibly common for even the most straightforward aspects of Christianity - for instance, literally its entire basis.
These can sometimes be understandable because some religious folks also hold onto some of these misunderstandings. A lot of work by apologists and pastors alike is done dispelling these false ideas from believers, but they can be pretty sticky. It also doesn't help that some of these false ideas are spread by pastors themselves. It can be really convoluted sometimes.
It is for this reason that I cannot in good conscious hold atheists and the like entirely responsible for their false beliefs. It is, however, always quite ironic when someone puts forth their reasoning for being against Christianity because of a reason that is not actually consistent with Christianity.
A good, straightforward example is the atheist who proclaims that Christians are only doing good things because they are either afraid of God if they do not or only because they selfishly believe they will be rewarded with heaven for doing these things, while of course the atheist is a good person out of pure and unadulterated altruism.
This is a misconception that many casually religious, vaguely Christian people believe, so again, I understand why many atheists would believe it - a lot of them were raised in vaguely Christian, holiday-only religious households. It also is in direct opposition to the bare basic teaching of Christianity.
A quick summary for you:
The entire basis of Christianity is that Jesus willingly died to save us from the consequences of our own sins. God sent His son Jesus to die on the cross for us in order to bridge the gap that we, flawed and broken people, could not. There is nothing that any of us individually could do to become righteous and pure because we are sinful people who have already sinned and are already guilty. Jesus took our place, He suffered God's wrath for us, so that we could be with God who loves us in heaven.
What this means is that if we were able to perform enough good deeds to cancel out our bad deeds, God would never have had to send Jesus in the first place. Jesus would have suffered and died for no reason. So, the false belief isn't even only just believing you should do good deeds to get into heaven, but that you even could perform good deeds to get into heaven. You can't.
Christians do good deeds because from love comes loves - the God who loves us calls us to do good, like His son Jesus. We are to be compelled by the love of God to also love one another. We are not even supposed to do good deeds out of guilt - we are called to do good, but unless it is done out of the love within our hearts, it's not the good we were called to do.
This misconception is directly at odds with what Christianity actually teaches. The love we were shown should compel us to do good to others, to show others the love of Jesus, out of love for them, not because we expect to be rewarded. You might as well not give at all if it is out of guilt or obligation.
Tying this together, misconceptions like these, while they are somewhat understandable to hold - especially for atheists who do not study and likely do not particularly care about these things - are usually found to be quite ironic.
Possibly the most used "argument", at least from my observation, against religion and of course Christianity specifically is the idea that the religious are merely believing what they have been told without ever questioning it. The idea is that if one were to actually question their religious beliefs (going off the idea that clearly no religious person has ever questioned their beliefs, as if that is believable...), they would realize they were silly and would become atheists. Even Richard Dawkins himself is short sighted enough to believe that all religious people are merely the religion of their upbringing, and that all religious beliefs are the result of being indoctrinated as a youth and not being smart enough to question what has been taught to them.
Without spending too much time on the easily demonstrable and statistical reality that unignorable numbers of people convert from the religion of their upbringing - both to other religions and to atheism - we can deflate this argument in other ways.
First of all, of course, is the logical fallacy aspect - it doesn't matter how or why people believe something, if it is the truth it will continue to be the truth, separate from the manner in which the people who believe that truth have come across it. If a homeless man in a tinfoil hat believes that he has found a cure for cancer during a meditation ritual he invented involving a dog's head and several unsavory dance moves, and that cure is in fact a cure for cancer, then that truth exists and persists regardless of the fact that it was discovered in a completely unorthodox and ridiculous way.
But the main point here, the irony, is that this argument can easily be turned around on the atheist or otherwise secular person in regards to the idea of the misconceptions discussed earlier. If someone is an atheist because he disagrees with Christianity due to false ideas that he holds about it, then it is entirely the same thing for this atheist to have merely attached himself steadfast to the beliefs he was taught without ever questioning them! If you have a distaste for Christianity due to something that is not even correct about Christianity, why is it that you have not taken the time to think for yourself, investigate the claims, and understand where these beliefs came from?
If you think the claims of Christianity are contradictory due to things that you read from atheist websites when you became old enough to question your vaguely religious upbringing, have you ever considered the possibility that these so-called contradictions are not even present in the doctrine of Christianity? Or did you merely believe these claims at face value because you heard them from a source that you trusted? Just as people tend to believe things they heard from a source they trusted, like their parents?
I was raised in a vaguely religious household. We did not even go to church on Christmas or Easter, as is the typical stereotype. The only time I went to a church was when someone died - I actually thought for a long time that churches were literally just for when people died. It was strange to me that they had such large parking lots and buildings, what could they possibly need all this space for?
Once I became older, I learned more vague and mostly false ideas about the concepts of God, heaven, hell, and spirituality from cartoons and other unreliable sources. My flimsy and poor religious education made it quite easy for just as flimsy atheists arguments to appeal to me. Like everyone else, I was taught that humans all evolved from other animals and that all creatures came into being this way, that the earth was formed naturally by some unknown cosmic accident (but it definitely wasn't God), and that supernatural things were not possible because they weren't natural. Without any actual religious background, it was quite simple for appeal-to-intelligence and appeal-to-authority atheist arguments to win me over as a young teenager.
It was obviously completely absurd to believe that God created the heavens and the earth. Why? Well, because I was taught in school that it happened naturally, somehow. My public elementary school definitely taught me the truth - and I believed it without ever questioning it! How ironic.
Yes, the irony lies cemented steadfast in the reality that much of the secular and atheist beliefs are believed by children at young ages because they are taught them in school, from TV, or other sources. People with strong religious upbringings will question them, and people with weak religious upbringings tend to attach themselves to them - especially if it's the only explanation to our existence that they have ever been given. If you're a fifth grader who has never actually wondered why our universe exists, and your teacher is the first person who tells you it was a natural cosmic accident, that's going to be what you're going to believe. It is literally the exact same as being told that God created the universe, and believing it.
Many atheists ironically do not realize that many of their own beliefs - both their beliefs about religion and their beliefs about naturalism - are beliefs that were fed to them that they accepted without question.
I became open to the idea of the existence of God once I actually began to question the atheistic dogma I had been taught - the beliefs that I had never questioned. I began to learn that the ideas I had about Christianity, about religion, and about God were also wrong - I had never questioned them either. I was guilty of this exact scenario which I have described, while simultaneously believing the same trite line - "religious people don't think for themselves."
Now that I think about it, it's rather ironic.