I am simultaneously angered and amused by Christians who are offended by various public things that atheists do. Christians are offended by the atheist bus ads (for example), taking them as an affront to their faith. In a way the ads are offering an alternative to Christianity, but they are extremely mild and positive and are in no way rude to Christians. They don't malign Christians or criticize faith. They say very little about Christianity at all, in fact and focus solely on the ideas and benefits of atheism. Compare that with the average church marquee that is laced with threats and condemnations.
The bus ads are not targeted to offend Christians or even to convert them. They are designed to promote discussion and to put atheists in a more positive light. They also function as a beacon for those on the edge (as nearly all atheists once were) of discovering the truth about God (he doesn't exist) but afraid that this discovery would ostracize them or even endanger their way of life. On the whole, I think they're working. I know better than to believe that the buffoons at Fox & Friends represent any sizable portion of Americans. They try to whip up anti-atheist sentiment (see the segment below that is neither Fair nor Balanced but unsurprising nonetheless) on the basis of a harmless ad ("You can be good without god"). I imagine that most people do what they do with all bus ads: ignore them.
Christianity has always been frightened and hostile to ideas. Virtually every single element of modern life (including our current version of Christianity) has been opposed by the religious. The rise in popularity of atheism and/or secularism is certainly no exception. And, for the record, I don't think that the atheists' agenda includes global conquest. Mine certainly doesn't, but then again, I don't speak for all atheists.