Anti-theism is troubling to me for a few reasons.
First, theism is a hugely heterogenous category and it just doesn't make sense to be against all theisms. With how heterogenous theism is, it is difficult to see an anti-theist as anything other than a person who has a limited understanding of theism. Often, I see the anti-theists as folks who had some bad experiences with a subset of theism, then take that hate and anger to an overgeneralized extreme. It is neither well-reasoned nor healthy to be doing that to me.
Second, suggesting everybody would be better off if they were just like me speaks of a desire to control what other people do and think that is troubling. I get that not everybody embraces pluralism as a proper family value, but whenever I see attempts to homogenize cultural diversity, it raises big red flags in my brain. It speaks to a level of arrogance and authoritarianism that I have a really hard time swallowing, even as I recognize that this sort of arrogance is almost universally human and part of all of us to some extent.
Last, and perhaps most importantly, I find it downright disturbing that anyone would be against expressions of value, wonder, and sacredness that bring so much positive influence to human lives and cultures. Do conflicts over what we value and find sacred pose significant challenges for human cultures? Of course they do. But to let this so completely overshadow the positives and try to rip a beautiful source of meaning out of someone else's life is, well... disgusting.
And, obviously, as a theist, I'm going to feel personally threatened by anybody who wants to wipe me or my ideas off the face of the planet. Call it a survival instinct. I'd hardly blame an atheist for having the same reaction to anti-atheism. Come to think of it, I have pretty much the same problems with anti-atheism that I do with anti-theism. Both smack a ridiculously heterogenous category, are much too authoritarian, and aim to destroy sources of meaning in people's lives. Both are equally troubling to me, and both speak of intolerance and bigotry to me.