Constantly laws are passed that curtail our rights. In God We Trust on the currency, Ten Commandments, Pledge of Allegiance, prayers in various forms of government, constant use of political power to get god into our lives from license plates to the crosses on the roads. Most of our attempts to fight back are foiled by the courts solidfying the positions of the religious right. So the question is are we second class citizens in this country? Blacks, gays, women have got their fair share of civil rights when will we get ours?
I agree hatred and discrimination of any type is wrong and should be stopped
The treatment of skeptics varies depending upon location, but it's nothing like what people face daily if they are women, people of color, queer, transgendered, women of color, queer women of color, etc.
All other things being equal, skeptics are not lacking any rights concerning what they do or do not believe--it's just that religious people (namely those on the right) possess certain PRIVILEGES that they should not have. Religious people should have the right to thought, belief, and gathering with like-minded individuals (such as worship)-nothing more, nothing less. They should NOT have the right to enforce their wrongheaded notions on others, pass magical beliefs into law, and all the other stupid crap they pull.
You might want to rethink your assertion that the problems suffered by "blacks, gays, and women" are over. Women are fighting back against an assault on basic medical care and bodily autonomy, a very personal invasion that most men have never encountered. Queer people still haven't convinced people that they deserve to have a life with the person they love in a way that is legally recognized as valid, the way straight people have always taken as a matter of course. People of color are often ghettoized, denied access to many amenities and opportunities that whites take for granted, and are racially profiled and victimized by the police. Our struggles are far from over. Also, your use of the phrases "fair share" and "when will we get ours" seem to suggest that you view civil rights as a pie, where if one group of people receives some of the pie (rights), there is now less pie to go around to other groups. It's not zero-sum. Rights are not a finite resource. If just civil rights are bestowed on a group of which I am not a part, I do not experience a curtailment of my freedoms. It needs to get better, but I feel that if it doesn't get better for everyone, then the whole thing was just worthless.