I'm a little hazy on what you mean. If you mean that persecution of atheists is wrong, then I wholeheartedly and sincerely agree. Moreover, I hope you would agree with me that persecution of any group is objectively wrong.
That being said, I do believe that atheism is inherently sinful, as sin is something that deteriorates one's relationship with God. Total rejection, I think you would agree, tends to deteriorate relationships.
Oh, yeah, I agree with you here. I just wanted to tie this back into the original question of why "atheists are thought ill of."
What I mean is that when a belief that something is wrong manifests as a judgment and persecution of the person,
that is when atheists (or believers) are thought ill of.
To further respond to the initial inquiry of the thread, as to
why it occurs, the can be generalized. It seems that people tend to see one difference between "their group" and "the opposing group" and also see other, more threatening differences where they don't appear.
This happens
all the time, for good
and for bad.
Take skin color. Many subconsciously assume that those who share our skin color share many other aspects of our personality or beliefs, which can manifest itself as "hanging around" others with our skin color. This is actually true to a certain extent, due to common sociological and other factors, but the perceived similarity--or, at least, the perception that we have more in common with those of our skin color than those who do not share our same skin color--is often overblown.
Throughout history, this has even been done with eye or hair color to a lesser extent.
(Speaking in the general "we" here: )
Since Christianity is associated with morality, if we're Christian, we assume other Christians to be moral as well. We also see these two similarities as interlinked; the perception can then arise that those without Christianity cannot be moral. And that's where atheists becoming "thought ill of" begins.