Here's just a few:

• Professor wins settlement against San Jose City College form wrongful firing after citing research related to possible links to hereditary and mother-fetus relations and sexual preference were found 'offensive' by a student
• Professor at Wheaton College fired after converting to Catholicism
• Veteran teacher cites pattern of religious antagonism by school administrators and claims they lead to her being fired

And here are examples of religious groups being nudged from the public square?

• New Jersey's A3371 Bill which "prohibit[s] attempts to change sexual orientation"
  • The bill's sponsor is on record equating sexual preference therapy to '[paying] somebody to beat or abuse your child' and suggests that the state should remove children from their parents who seek such therapy options.
  • A great article exploring some of the ramifications of such a bill--basically it challenges the very notion of self determination (mind over matter)
• A school girl was forbidden from choosing "God" as the subject for a writing assignment that told the kids to write about their 'idol' in life--the school later apologized for incident saying that violated the girl's right to free expression
• Christian protestor at gay pride event has sign forcibly removed from him, tackled, the punched several times
  • Video of the assult

There are many more examples, but these are just a few from a variety of contexts.

Now, please don't think my citing these articles means that I think religious people are persecuted in any way comparable to those in the world who actually risk their life by openly practicing their religion. However, we simply cannot ignore these kinds of incidences and pretend that everything is okay or that trends aren't materializing.

Please also don't think this means that I think the persecution is one sided. Religious and non religious people have a long and tragic history of misunderstanding each other and letting their emotions get the best of them as that tension sparks violence. As a freedom-loving society, we all have a responsibility to look out for instances where the freedom of an individual or group is threatened since that erosion of freedom directly affects everyone's freedom.

Some comments on these specific examples:

• San Jose City College settlement - this highlights the problem when a population equates political correctness with morality. It leads to individuals going around taking deep offense that someone would dare even suggest an opinion that they feel isn't sensible or already accepted. On the specific issue of biology and sexual preference, we (humanity) simply don't know enough to have an informed opinion or to have any policies on the issue. It's entirely possible that it could originate from some specific combinations of genes, neurology, and/or upbringing. If not, then where does it come, a soul? These are tough questions that are far from black and white.
• Wheaton College firing - this one was actually a religion-on-religion intolerance and highlights that religious intolerance is hardly an atheist vs. religion problem but is a human problem. I didn't look for a specific example of non-religious vs non-religious intolerance, but any search for socio-political violence sure shows how any group of people can resort to violence if they allow their emotions to get the best of them. BTW, BYU isn't perfect in this matter either.
• Veteran teacher cites religious intolerance for her firing - this is just an allegation, but worth noting. As a Mormon I've taking some little jabs in the workplace because I don't drink or because I have more 'traditional' views (which, BTW, is contextual to where you live since when I lived in Utah I was considered liberal). I've also overheard co-workers say some pretty intolerant things about religious people in general (one of whom was fired for making statements like that -- though I had nothing to do with that). I guess I could stand up and make a scene, but my approach is instead to strive to have positive relationships with those individuals. Fortunately, I haven't encountered people who were antagonistic towards even that approach. Who knows, perhaps that was the situation here.
• New Jersey's A3371 bill - This is just an awful bill. It's not awful because it does provide some protection for minors against a therapy that can be abusively applied. It's an awful bill because it legally mandates the rejection of the philosophy of self-determination. It's just an example of when blind adherence to political correctness leads to irrational and amoral behavior. It smells of blind naturalistic reductionism.
• School girl writing about God - This one has a happy ending. The school took the right course of action and 1) admitted that "no laws or district policies allow teachers to limit students’ expression of religious beliefs in their personal classwork." 2) Called the incident a "regrettable misunderstanding" that they "must learn from" and 4) Didn't fire the teacher over the incident and instead sat everyone down to have a positive conversation. This example highlights the hypocrisy of such groups as Freedom From Religion Foundation. When we seek to anesthetize the human experience we weaken it for everyone. A large part of being a well-adjusted human is finding the beauty in the world around us, especially when we may have objections to other people or ideas.
• Christian protestor beaten at gay pride event - The question arises, "What would headlines be if the roles were reversed?" We don't know, but this event highlights that the desire to silence those with whom you disagree with is fundamentally a human vice, no a religious or non-religious vice.