As someone who's had an atheist background, I'd say that most atheists speak out against Christianity for a few reasons.
For starters, as a Roman Catholic, I felt incredibly alienated and repressed as an individual. Constantly had I, personally, been shot down for answers to questions, been humiliated in front of a class by a Catholic Teacher, and been told that I'm hellbound hundreds, if not thousands, of times. This notably created distaste for, specifically, the Roman Catholic Denomination of Christianity and after this, when I went to Jewish Orthodoxy (at a mother's prompting -- I being quite young at this time) I commonly spoke against Christianity even then.
But as time goes on, and when I geared towards a more atheistic view, I spoke out about Christianity mostly out of a... well, a small fear in the political and educational scene. Many schools were pushing for teaching creationism, teaching of Christian values and demonizing all else in the process. At the same time, there were many (and still are) fundamentalist right wingers who wanted to enact Christian laws into secular law. (Meaning, I'd be forced to follow them). Some of the proposed laws were ludicrous to me, so I started to formulate arguments against them and began to learn Christianity in more depth (as, in arguing with any strict-adherents of the faith, I would need to know the faith).
Even later on, I learned about Evangelists, Jehova's Witnesses and even random Christians at public schools I went to, who would all try to convert me to their faith. Often times I had to, perhaps not too kindly, tell them to back off. Naturally, all of these experiences created a particular dislike towards Christianity (mostly, the faith and the extremists of the scene) as I hadn't met any Jews or even Muslims who had a chance of enacting similar change. In fact, I met a few Christians who explicitly said they want America to be a Theocracy, and that they would happily kill all the heathens and "sinners."
So in short, it mostly has to do with past experiences, or the power of the Christian religion in the world at this time, or the evangelists who like to throw things at people, or a combination thereof (or even other reasons). This is based on my personal experiences, and I still often speak out against Christianity in terms of media and politics because in being a Satanist, Christians demonize the faith and use whatever they can to make it seem horrific (There are plenty who don't, and I respect them for that), and there are many Christians who push for Gay Marriage to never be legal (or believe that if made legal, Churches would be forced to conduct them -- they wouldn't, it'd be optional for churches) which directly affects me, and many Christians pushed for the DADT ruling to stay in the military (Which, I intend to be a part of in the near future, so such a rule would have basically meant that I couldn't have a significant other for the four years I intend to serve in the USAF).
That's primarily why. I also wouldn't like Islamic extremism, or Judaic extremism. Pagans, even Wiccans, tend to be a lot more liberal and tend to be a lot more diverse in belief to the point where, even if they lobbied in the political realm, odds of it bringing harm to other minorities is relatively low and there isn't a huge following for those faiths, unlike with Christianity.
Now, this is just me. I don't claim to represent all atheists, or all Satanists, and I don't claim to be representing anyone outside of myself (for, that is all I have the authority to represent).
On a side note: I try to study and understand the Christian faith, before saying anything about it. I know many denominations believe differently, which means I just need to keep up to date as much as possible, and I do respect many, many Christians, Jews and Muslims I have met and have, personally, found them to be great individuals. So when I say something against the "faith" I don't mean to hold it personally against individuals, same when I refer to fundamentalists and extremists. When referring to the preaching, I dislike the act of preaching, not necessarily the person. (Many a time has what I said offended individuals for some reason, so this is my attempt to avoid it if my post above came off confrontational in any way -- I tried to keep it as neutral as I could, to answer the question and to also throw out the notion that "all atheists hate Christians" or the more common "all Satanists hate Christians" that crops up in discussion a lot.)
