Look at it this way: He could be judging you for something you have no control over, such as your skin color or your family's religion or how much money you have or what your brother does for a living. Judging someone on the basis of his entertainment choices is, in contrast, quite enlightened, and the reason is that is at least that is something that's your choice. And you, of course, are at liberty to judge him for his choices as well. So however annoying it might be, and I am sure it's very annoying, judging people for the choices they make is a perfectly legitimate thing to do. He could do a better job of selecting the choices he uses as a basis for his judgments, IMO, but hey, he could do worse.
People judge other people all the time. That's just the way it is. If he's going to let a silly thing like Trek color his whole attitude toward you, than that's his problem, not yours. If I were you, and in some ways I am you, I'd bask in the glow of my own geekiness. Geek pride!