While I wrote this to address theists, I think the points made can show atheists that not wanting to offend religious people might not make as much sense as they thought.
Do those 'new atheists' really get on your nerves? Questioning your deeply held beliefs, even making fun of them? Do you feel offended and deeply hurt when you find you can't share your faith without someone trying to show you're wrong? These are daily challenges religious people have to face in this increasingly secular world. Buses with atheist adverts, books attacking religion, more and more people being outspoken with their views on god belief.
While you may not show it with any kind of outburst or violence, the way many atheists are acting today might still be affecting you, making you feel angry and frustrated. Should you be affected like that, considering the beliefs you hold?
You might find it useful to follow the better guidelines in the Bible and forgive those people, or be slow to anger and turn the other cheek. But if it is difficult, keep in mind that if you are going to live forever in heaven, all the grievances in this life, including having to deal with these atheists, will soon become a distant memory. Even if it takes a million years to get over it, that's still not even a drop in the ocean compared to your eternal existence.
A billion years, 10 billion years, what does it matter? If the offense and emotional pain lasts this long, which is doubtful - think of what might have offended you five years ago and you'll have trouble - compared to an eternity, billions of years can't even be compared to an atom in the universe.
So, don't feel too bad. Just keep in mind this whole business should barely register if this is just the start of your gazillion billion trillion zillion zillion years times infinity existence, and it's strange why you would think in such a short term way.
In the grand scheme of things, what possible difference can anything that goes on in the secular world make? Not only will you be living forever in bliss, depending on the specific religion you follow, you might also believe Jesus will be returning to Earth and making it a Christians-only planet. Or that Allah will make this a Muslims-only planet. Or something similar.
Anyone who's gone against your god will be judged and punished by him. Not wanting children taught creationism, seeking equal rights for women and homosexuals, promoting condom use, allowing abortions, euthanasia, stem cell research. If any of these things are wrong, your god will make sure they understand this.
With atheists and other non-Christians/non-Muslims/others (delete as appropriate) being wiped out by God, leaving Christians/Muslims/others (delete as appropriate) to rule the planet, how can you possibly feel offended by what they do in the here and now? It makes no sense.
Only those who know deep down in their subconscious that their religion is a lie could feel any offense, because they might not want to lose the comfort it brings them. True believers shouldn't be concerned in the slightest. Why should you be?