I think many people associate negativity with atheism because there are many atheists out there who are in general rude and judgmental towards people of faith, calling their beliefs stupid, irrational, etc. Then again, the same could be said about many overzealous religious people towards atheists, which is why many atheists also associate negativity with religion. There’s a difference between having a spirited debate on the subject and being insulting about it, there’s a thin line and many people often cross it when discussing it.
I would probably consider myself an atheist, possibly agnostic, and I have no real problem with people who believe in God or a higher being. However, I do have a problem with people trying to shove their beliefs on me and make me believe what they think is correct, and I think that’s where a lot of religious people and atheists are coming from with their negative connotation on either side. It pretty much goes both ways. Many religious people would say to atheists, “Oh, you’re going to Hell because you don’t believe in God and you don’t follow the Ten Commandments!” But that’s not to say all religious people are like that, not even close. On the other hand, many atheists would say to a religious person, “Oh, you’re so dumb because you believe in God. Why would you believe something so ridiculous, it’s like believing in Santa Claus or the Easter Bunny!” Again, not all atheists are like this, I wouldn’t even say the majority are like that. But it’s the people that do act like that, who are self-righteous about their beliefs and look down upon those who don’t agree, that give the concept a bad name.
Another reason for it might be that for thousands of years, a majority of societies were mainly, if not completely, religion based, and not believing in a God was practically unheard of. Often times, it was even considered a crime not to believe in God. I think the fact that atheism has been a much more recent development than religion is where a lot of religious families/people get the idea that it’s “bad.” It’s much like the conflict about homosexuals. For thousands of years, no one would even think of not being attracted to the opposite sex, or at least admit it. Being “straight” was the established norm, and being gay was “weird” or “ridiculous” or “just a phase.” But as time goes on, sure enough, much of society is more accepting of the idea. Religion is a much more established belief, and I think in the future, once it becomes more commonplace and people get used to the idea, atheism might be more accepted in society as well.