Many atheists understand this. Honestly I think that religious people suffer from the same delusion as atheists. Just like the atheists see religious extremists and tend to over look the rest of the religious moderates around him, Christians, Islamists, etc. see only the atheists that openly taunt and threaten them (whether or not the threat is real or perceived).
I would wager that most atheists are not that extreme. They were brought up and now live in a world seeped with religion. Those that live in areas where religion is repressive learn to hide it while those in the developed world (especially the US) usually have to adapt. Likewise much of the people in the US have no problem with atheists. Many will be confused or question your decision, maybe be a bit condescending, but few will be spiteful. Atheists make up 14% of the population. They may be concentrated in the West and East but they are nonetheless everywhere. I know many Christian families that grew when one of their family members came out as an atheist and they had to deal with an entirely different world view (and often a different view on knowledge and faith), even if it was in the teen rebellion stage of atheism.
I know many extreme atheists and even they dont lack empathy for the religious or their religion. They're extremist because (this is my hypothesis based on nothing more than self reflection) atheists see the possibility for the same fulfillment, morality, and answers in a different world view, one that is largely naturalistic and does not come with the "moral baggage" of ancient (and largely static) religions and philosophies. This view, however, is shared by relatively few people, seemingly in growing numbers, and the few have to be vocal.