The Washington, D.C.-based United Coalition of Reason filed the lawsuit in U.S. District Court, describing an ad-buying effort that started in 2011. Late that year, according to the complaint, the organization reached out to Port Authority and asked to place on buses an ad that “consisted of a background of blue sky and white clouds with the following text: ‘Don’t believe in God? You are not alone,’ and the website address of a local group.”
According to the complaint, Port Authority attorney Michael Cetra rejected the proposed ad, indicating that the agency doesn’t run “non-commercial” material.
If you click on the above link, you'll see a Port Authority bus bearing an informational advertisement for Pennsylvania's suspended Voter ID law. I'm pretty sure that qualifies as "non-commercial" material.
And that's why the Port Authority should just run the UCR's ad, because they're very likely to lose the lawsuit.