A New Kind of Intolerance?

Here's a story that made me sad. If you don't have time to read it, let it suffice to say that a teenaged girl,  Jessica Ahlquist, went to court against her school in order to have a banner removed from the wall -- a prayer that had been written by a former student of the school and that had hung on the wall in the place for forty-nine years -- and she won. Ahlquist is an atheist and she found the prayer offensive.

Some have labeled this girl as "evil" and others have lauded her as a champion of the ideal of "separation of church and state" that is contained in the first amendment of the United States Constitution.

I have always been mystified by people's interpretation of this short passage:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof [my italics]; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the government for a redress of grievances.