"Non-religion" a protected class

On Tuesday Madison, Wisconsin, became the first city to ban discrimination against "atheists". "'Nonreligion' was added as a protected class by the Common Council under the city's equal opportunity ordinance."

According to former Atheists Humanists and Agnostics president Chris Calvey, "Having it on the books, where we're legally a protected class, that'll make things much easier for atheists. And we'll be able to be confident that at least if we're honest about what we actually believe, then we have the law backing us up so we can't legally be discriminated against."

Now the atheist -- the final wording was actually "non-religion" -- is a "protected class" right along with sex, race, religion, color, national origin or ancestry, citizenship status, age, handicap/disability, marital status, source of income, arrest record, conviction record, less than honorable discharge, physical appearance, sexual orientation, gender identity, genetic identity, political beliefs, familial status, student status, domestic partner status, receipt of rental assistance, the fact that the person declines to disclose their social security number, and unemployment status. 

My first reaction is to wonder whether Madison had been discriminating against atheists all along until now? 

Second, I guess I'm too slow to grasp the whole concept of "protected class membership." Does that mean that those not listed in the protected classes don't get the city's protections? Or that those in the protected classes gets a better version of protection from the city?

Pity the poor folks who don't belong to a class.