I never thought of the term "rat rod" as a negative. I think it started in the bike hobby, where the term "rat bike" was in use, long before I ever heard it used for cars....but the build style is the same: weathered finish...vintage parts...and minimalistic. :-)
Once the term surfaced in cars, I think the problem was that the younger guys who liked the style seemed to take the name as a criticism or judgement.
Some of the boys in our family (who I love very much) are always looking for someone to insult them so they can make an issue of it. It's a social issue that seems to have gotten worse since another term, "dis" or "disrespect", became popular. I find that if you look for something long enough, you will even find it where it doesn't exist. I believe that "rat rod" is taken as an insult much more often than it is ever meant that way. Too bad. If a guy is really selfconfident, he doesn't even give too much value to others opinions, so it never gets to the point of angering him.
I personally like the term, as it is a funny way of describing the deteriorated or worn look of the car. I also like the imagination I see in them, as the enthusiasts who have long term involvement tend to become more "generic" in their building style.