I know this is going to get me into trouble, but...
As an atheist, I have been told by multiple Christians multiple times that:
1. I'm going to hell since I don't believe in their god
This has nothing to do with saying that you are inferior, immoral, or capable of being good.
2. I cannot have a moral compass without religion
Lack of a moral compass has nothing to do with being inferior, immoral, or capability of being good. It means that you don't have a proper frame of reference. Anyone walking east in this country can reach the Atlantic Ocean, whether you have a reference or not.
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3. I am stupid for not agreeing with them that the wonders of the universe could only have bee created by God.
Stupid denotes a lack of knowledge, but has nothing to do with being inferior, immoral, or capable of being good.
4. I've also had children at school tell my kids they can't play with them because they don't go to church.
And that, again, has nothing to do with you being inferior, immoral, or capability to do go. It is what you believe that they think of you, but nothing that they have told you. You are infering that based on your own biases. Perhaps it is merely that your children, not attending church, does not allow those other children's parents a frame of reference for your children's upbringing, and therefore they do not want their children to potentially be led down a negative path.
So in my experience, all of the above does happen quite regularly. I absolutely agree that the central tenet of Christianity is to "love thy neighbor", but it seems that many have missed this lesson.
Or, like another tenet of Christianity, that all are sinners and fall short of the glory of God.