That's my take on it and for those who think of me naive about life, I'm sorry that there is know way I could convince you otherwise.
My take on 'religion', in general, is that it's not inherently bad but it is used as an excuse by people to do things which would otherwise be clearly wrong. It doesn't have to be religion for this to happen, either - you might see the same thing happen with a guy or a group of guys trying to impress some girl. Or somebody slapping around somebody else because they don't like them, even though that person has never actually done anything to hurt anyone.
Of course just to complicate things, there are some moral systems and justifications where you can easily justify those things as being the right things to do. Granted, you might get caught up in ends-justify-means reasoning and most people might not agree with you, but anyway...
Both the strength of and the problem with religion is that it links things to a higher meaning. You can't question God. You can question the interpretation of God, sure, but once you say that God meant something, you can't question that. And that can be a good thing - somebody might go through life being happy because they believe that God has a plan for them, and that might get them through rough spots in much better steed than somebody who doesn't have that faith.
But that can also lead to abuse, when somebody says that God is against this. Suddenly, whether something is immoral, whether it forces you to do injustice against your fellow man, doesn't really matter. With the mandate of God on your side, you can do pretty much whatever you want. The ends do justify the means, and no man or mortal can question what you are doing because God automatically supersedes everything material. If you are fighting for a truly righteous cause, then that is your strength. If your understanding is corrupted, the teachings that have been given to you have been perverted, or if you simply use that mandate as a rationalization rather than true purpose, it is a terrible thing and will lead to all sorts of senseless wrong.
And sometimes, religion is just insensitive to other people. Whether that is something simply added in by the human authors of holy works or by the diety that inspired them, it can lead to people going on a crusade against people for no other reason than simply because they believe that it is 'right', because their religion defines their morality and they never go any further than that.
I'm not exactly sure how I can make my point any further other than to say that I think that there is a difference in the type of people that become atheists, and the type of people that follow religion, in terms of how they go about things. Generally, people who follow religion end up getting accused of being sheepies, while atheists end up getting accused of being cold or negative. My suspicion is that atheists tend to value independent critical thinking over group harmony, while religion tends to be the other way around. Those kinds of subtleties are usually lost once a discussion gets heated enough.
It is interesting to note that there are Christian philosophers who attempted to formulate Christian morality, etc. without relying on the bible, though, so it's not like challenging religion is exclusive to atheists. The difference being that I've gotten the impression that religious philosophers start from the premise that religion is true and try to prove it, while atheist philosphers go the other way around, and start from the premises and try to formulate a conclusion.
However that is totally opinion and I've done very little checking on that last bit, but I figured it would be interesting to toss that into the discussion and see what people thought of it.