In spite of the way the word "apology" is used now, Christian apologetics aren't apologizing for their faith, or its existence, or its past excesses (such as the Inquisition or witch hunts). As they use the term, it comes directly from the Greek word apologia (απολογία), which means in defense of; someone summoned to an ancient Greek court to face a charge would present an "apology" or a defense. Christian apologetics start by arguing that "Christianity is reasonable and in accordance with the evidence that can be examined, analogous to the use of the term in the Apology of Socrates, written by Plato." (Wikipedia) From there, apologetics becomes the attempt to defend Christianity and establish its truth, using reason, evidence, and scripture. At its far reaches, it appears to blend into evangelism, when it becomes "the work of convincing people to change their views" and moves from defending Christianity to requiring the questioner to defend his own faith against the apologetic message.
Amusingly enough, although apologetics developed with the first apostles and was part of the church before the Protestant Reformation, Christian apologetics now defend "their" faith against Roman Catholics, in addition to Mormons, Muslims, and atheists.