If you took some time to find out what the exercise was about, you'd know that the intention was to make a point about the significance we often attach to symbols. The fact that you are here calling him an "intolerant coward" kind of proves his point.
I can only guess that your single source of information is something like FOX News. The reality of the exercise is that students are asked to step, not "stomp," on the paper and the expectation is that most of them will not do it. This therein is the foundation for generating a conversation about symbols and communication. That conversation is a good one and an important one, as evidenced by the fact that the professor in question has received death threats, and there are of course plenty of other examples of real or threatened violence being directed at individuals who have desecrated such symbols.
It's also really important to point out the context. We aren't talking about high school kids. These are adults and part of the point of college (hopefully anyway) is to provide a challenging environment. That is sometimes difficult. That's a good thing. None of them were forced to be there, forced to write on the paper, or to step on it. No one was disallowed from objecting or from shouting their dismay at such a suggestion.
I don't know, perhaps you'd prefer good little puppets who walk around dutifully following the word of whatever God you believe in. Not everybody does. Some of us want adults who think for themselves. Some of us want adults who will step on that paper and say, "it's just a piece of frickin' paper." Some of us want adults who will say, "heck no it isn't just a piece of paper." The point is we should all want adults who understand the world is full of lots of different people who need to learn how to sit down, have a conversation, and then together get where we are going.
It might also interest you to know that the professor is a Christian and the exercise comes from a textbook written by a professor who teaches at a Catholic university.