As both an atheist and a moderate antitheist and perhaps most importantly a skeptic, it is not so much Christians (or other religious followers) that are "hated" as it is the idea of any religion.
Skeptics/atheists/antitheists/etc generally believe religion to be a danger and detriment to the continuing advancement of society. Thus, most are against not just Christianity, but are also against Judaism, Islam, Hinduism, Scientology, etc. These are theistic doctrines (meaning there is a belief in a deity or deities), and possess many inherent creationist beliefs, and other beliefs that are in direct contradiction to quantifiable scientific evidence.
The cause for concern of religion as being dangerous lies in the fact that many people are willing to turn a blind eye to measurable, quantifiable, reliable research, evidence, and fact, in order to preserve religious beliefs. Science and reason are open and accepting to change in the face of new evidence, while most religions are unwilling to compromise in similar fashion.
Belief in science and reason is also frequently in contrast to religious beliefs because it can be difficult or even impossible to "reason" with theists concerning matters which are controversial only because they compromise religious doctrine, e.g. stem cell research, creationism and evolution, global warming, etc.
There are several reasons why it can appear as though only Christians are targets of antitheism. First, Christianity is the world's largest religion, and thus is typically the first target. If you live in an English-speaking country, Christianity is also most likely the predominant religion in your country. If this is the case, then there are more likely to be critics of Christianity because it is primarily Christianity that motivates these critics.
Also, if you are referring specifically to internet atheists, many of the most vocal opinions are also strongly opposed to the Bush administration, which is dangerously close to being a theocracy, and as such, its inherent "Christian" properties inspire the greatest disdain, thus making Christianity appear often as the lone target of antitheism. Lastly, some critics of Christianity fear it is not politically correct to criticize Judaism and Islam, and thus often refrain from doing so.
Also worth noting is Buddhism (a major world religion) is rarely a target of antitheism because it is not a theistic religion.
It is only fair to keep in mind that "internet athesists" are not representative of atheists in as a whole.