I love the term nerd, and etc personally. I refer to myself as a nerd, and i love having 'nerdy' friends that are into the same things I am. If i were to call people a nerd, or a geek, etc, it would be affectionately. People referred to as geeks, are usually intellectuals, or love learning etc; but they're not that one dimensional. There's no reason to make these negative things. I have never been in an environment where those things were bad, nor would I have cared. Personally I just like to be around people that accept me for who I am, and if they don't , I have no interest in them. It just kind of seems like you came across people who made this a negative thing, when most people actually don't think that way. In terms of younger people, most of them are really immature, and find any reason to be mean to others. They're all idiots, and you really shouldn't take anything people like that say to heart.
I don't really know where you are getting this information that those words mean all those things that you said, I think you've just been made to believe that by people that are not so great people. I don't think it completely puts people in a box or anything. If someone hears the term nerd, and stereotypes a person based on that; that's their problem. There are just people out there, that can't see beyond. They're the kind of people who also just listen to whatever everyone else says, and can't have their own opinion sometimes.
Furthermore, I think I'm a nerd, but I have tons of other interests. I really don't care if there are small minded people out there, who see I have some kind of interest like gaming, comics, etc, and think that is all there is to me. Not everyone's going to like you anyways. I think you need to surround yourself with better, more positive, more mature individuals.I pretty much wouldn't use the media as a reference for anything also.