All that said I think atheists run into the problem of not their behavior but rather the behavior of "that guy". You know him. Maybe you are him. It's "that guy who can't shut up and says insulting things about people who believe in anything spiritual at all" But "that guy" is a pain to be around. I worked with "that guy" once and hearing him compare my beliefs to the flying spaghetti monster was pretty ignorant and if I valued his opinion more than I do would have been insulting. He would repeat this week after week seemingly escalating his rhetoric to upset me. I have long since worked out how I feel about all this so I held my own just fine. My only point in mentioning him is that for another person this might have been pretty annoying and upsetting.
I've run into "that guy" on multiple occasions-enough to notice who he is and steer clear at parties and at work. The only advice I have for you is if you are that guy or find yourself being that guy just stop. You're giving all reasonable, just don't believe in God but don't want to hassle you non-believers a really bad name. Though so do Sam Harris and Dawkins so maybe you should avoid them too.