Should the Establishment Clause Apply to Atheists as well?

Here. 

The majority view seems to me that it should be. If this conclusion is drawn, then what happens to Peter Boghossian, who uses his position as a professor at Portland State University, to promote atheism?

Is there a double standard in the way that academic freedom is typically understood? If I made it my stated purpose to convert my students to Christianity, and said so, (something I would never do) would I be more likely to get in trouble with administration than someone like Boghossian, who does what he does?