What difference does it make now that he changed his t-shirt? Everyone still saw him wearing it originally. Just because he covered it before boarding the a/c, does that make him less of a "threat"? Either deny boarding or don't, but if he's gonna get on the plane, don't stifle his free speech. There are no if's and's or but's when it comes to our Constitutional rights.
Please do not take this as an attack towards JetBlue (as I'm sure my airline of choice would've handled the situation in a similar manner), but rather the state of our country and the industry in general.