There are lots of examples of scare quotes being misused, as though they conveyed emphasis rather than irony.
But in an article that appeared today on the Indianapolis Star website, I am sure they are being used appropriately.
The title of the article is: “Indiana pastors to protest change in ‘religious freedom’ law.”
Religious freedom doesn’t mean expecting your voice to be the only one. It means recognizing that your own religious freedom is protected by the same laws that protect those with whom you disagree.
This image seems to grasp the point well: