Matt, not following how you could continue to foster and grow a discussion on religious tolerance/intolerance and set the rules as no scripture. For those that are religious, scripture is the basis of belief - whatever scripture they use. So essentially you're saying that we can only have the conversation from the atheist perspective (i.e. no scripture). That's not a discussion at all, merely a re-framing of the argument to conform to your own particular view.
I find no truth in bashing a faith or lack of faith on the basis of the actions of its followers. In rhetoric/logic/philosophy that's called an ad hominim, or attack on the person. I may have bounced a check once or twice in my life, but the rules of math are still valid, and I'm not disqualified from teaching them to my children. Truth is truth, regardless of whose grubby paws are holding it, so rather than debating the intolerance of the practitioners of a faith, how about we discuss the intolerance of the faith itself as revealed by its foundational writings? Oh wait, that's off limits. Seriously, what do you hope to accomplish here besides silencing opposition?
The irony here is that the atheist billboard specifically targeted the Christian faith, as if the atheist position has no message other than an anti-message. And their justification for doing so is on the basis of historical human suffering in the name of a faith? As if no atheist in the history of mankind has ever done anything wrong? Really, practitioners of atheism hold a perfect ethical high ground? That'd be a ludicrous claim, and I wouldn't think any would have the audacity to say as much. It appears the atheist cosmology is simply that anyone who thinks there is a God is unreasonable, or more accurately irrational, and prone to violence. At its essence, atheism cannot exist without theists to oppose ... lexically 'a'-'theism' = against a belief in God. Not a belief in something else, just an opposition to an idea. So I am supposed to believe that a world view founded on the principle of opposition is logically and ethically superior to a world view that is founded on the principle of the existence of God? Your worldview couldn't exist without mine, so merely on the basis of an a priori principle, the atheist is left only to attempt to disprove the causal argument with no actual statement of their own.
In the free marketplace of ideas, truth will out, so billboards don't worry me at all, and atheists in general represent no threat to my security. Of course, you can't have a free marketplace of ideas if one idea is not allowed to be expressed, so if the atheist agenda is to silence theists, then a line has been crossed.