I still don't agree that the Constitution inherently applies to private enterprise. I'm not allowed to use the ladies locker room when I go to the gym. That's sexual discrimination! The corner grocer doesn't carry matzo -- anti-Semitism!
But here's your blanket rule for you, even applied: "You can't wear clothing that is offensive or would lead passengers to believe you may be a threat to their safety."
That's the issue here, and if the case had been properly articulated I think the outcome might've been different.
Let me put it to you this way. If a passenger boarded an El Al flight in New York with a swastika emblazoned across his T-shirt, do you think if would be out of line to ask him to cover it up? Absolutely not. But then, people aren't afraid of offending Nazis, are they?