Atheism (or agnosticism) is tolerated far less than most deity-based religions within the USA, at least as far as I can see. I suspect the reason for this lies within the false feeling of persecution by theists. After all, atheism is essentially based around one thing: Logic and observation. And sadly, logical reasoning is the Achilles heel of many a major religion, since any form of common sense just doesn't seem to reach the same conclusion as they're trying to convey as 'supreme truth'.
Let's take this into an everyday scenario; one at a workplace, in fact. One employee talks about religion a lot, has scripture quotes hanging all over their office, wears a cross around their necks.. In fact, they even have a few tattoos quoting scripture. This is considered acceptable in most companies. Now, at this same company, an employee comes in wearing a T-shirt saying "Darwin is my homeboy". He gets asked to change his shirt because "coworkers are taking offense". Mind you, this is not a hypothetical, I've seen this very thing happen at a local store. I've also seen a similar attitude in many, many more places.
Again; it all seems to come back to theists seemingly feeling like they're being persecuted, and it's understandable, of course - modern science debunks more and more of religions' fallacies. But this irrational panic is just insane, and spreading fast; church leaders proclaiming there's a 'war on Christianity', saying there's a 'jihad against our church', trying to lead people to believe there's something like an ethnic cleansing going on? When you live in a country ruled by the 44th openly theist president in a row, you're a long ways away from that.