First of all, the Puffington Host (inside joke, I won't bother explaining it) is not the most neutral source, but let's dive in:
Atheists don't really face discrimination per se. People make a judgment to like them or not.
Atheists are a minority. Less than 15% of the country or so, but more than certain ethnic and religious groups that have similar problems with discrimination (Asians and Jews, for instance,) atheists have certain issues in America and elsewhere. Unfortunately for this article, atheism is a profound conscious choice. Those raised Jewish, for instance, who become something else later in life were still raised under an embedded culture going back thousands of years (and a lot of discrimination, persecution, and genocide in that history.) Atheism isn't a culture. It's a difference. A difference people are allowed to voice their dislike for. This is why homosexuals are right to voice discrimination, as it's not a choice to them whom they love. But atheism is a choice, a profound life choice. One somebody makes as an adult generally. And since it is not considered a religion, it can't get religious protections either. The best similar thing I can compare it to is being a vegan or a vegetarian.
It doesn't help that the biggest "advocates" of atheism are all pretty much smug jerks.
I was raised Moravian and became Lutheran latter in life. I have a general "Let it ride" attitude on religion. Don't throw it in my face or try to convince me how great your religion (or lack thereof) is, and you and I will not have a problem.
Comparing Atheism to being vegan is pretty off base.
Choosing your diet is not the same as choosing how you perceive the workings of the universe.
Nearly every Atheist over the age of twenty I have ever met is the furthest thing from a smug jerk about what they believe, only the young naive people are assholes about it, but they are that way regardless of their beliefs.
A belief system is a belief system.
Atheism is not a "difference" any more than any religion out there is a difference from it's predecessors.
Calling it a difference is implying that it only exists to oppose the other options, and also suggests an aggressive stance.
Just because Atheism hasn't been a dominant belief system for thousands of years like many others doesn't mean it can just be cast aside as some "difference" to the others that shouldn't be taken seriously.
Speaking they way you do about Atheism is exactly the way you are claiming "smug Atheist jerks" speak regarding other religions.
You are entitled to any opinion you may have, but throwing half thought out, hypocritical crap about something that you clearly have very little knowledge of is not the way to be taken seriously.