They took a DNA sample from Karr. It did not match the DNA in the underwear. That proved he was not the killer (even if he WAS in the state of CO!) and he was not charged because of this fact.
I'm sorry, that seems really silly to me. If he had been in Colorado and if his handwriting matched that of the ransom note then I can't see how because some DNA skin cells didn't match that he would be exonerated, especially since he confessed.
The DNA cannot be conclusively proven to be the killer just by virtue of its existance. It isn't semen or saliva so it doesn't substantiate that the owner of the DNA committed the sexual assault. It could have come from any number of modes of transfer.
I mean, if the DNA belongs to some man who was on stage during the entire timeframe for JonBenet's murder, what do you want to do, arrest him for it even though he cannot physically have killed??