They reached this conclusion in much the same way you do when playing Clue: They just picked a guy and guessed. They literally had no new evidence; they just felt like giving slander a try in a bid for ratings.
The whole JonBenet cottage industry is a lot like the movie version of Clue, now that I think about it. We have the details of a crime, now let's just run through a bunch of alternate endings in which it's more or less plausible that each new person we accuse did it, and that'll be super entertaining. The 2017 documentary which will air on Netflix is described as a "vision of a mythic American tragedy." But it's not a mythic American tragedy. It's the personal tragedy of a family who have to keep living through it 20 years later. Imagine if your child was killed, and for 20 goddamn years, no one would stop talking about it ... or accusing you of doing it, despite the fact that you'd been eliminated as a suspect by the district attorney. How do you manage to keep going through your days with this shit tossed in your face endlessly?
Obviously, many people still believe the family was involved. But it's been 20 years. They're not being found any more or less guilty. There's no new evidence. Unless someone confesses or a witness somehow comes out of the woodwork, this is it. The story is over, and has been for a long time. Even OJ Simpson didn't get as many TV movies made about him, and they at least had a crime, a car chase, a huge trial, and all kinds of media-fueled drama to pad the plot of those.
Just remember this column when JonBenet -- America's Daughter: American Crime Story gets announced.
The sad truth is that these movies or pseudo-documentaries are by and large not really concerned with the truth of the story. They're not here to add depth and context and insight. They're the "reality" version of a CBS procedural drama, endlessly played over with predictability and time-tested formulas. They're CSI with real victims. People are entertained by them. Child beauty queen, a rich family, a sinister crime with crazy details like a suspect ransom note, a curious 911 call, and hints of potential sexual and physical abuse. If it wasn't real, it'd make a perfect Special Victims Unit episode, wouldn't it? Oh man, how will Ice-T get to the bottom of this one?
You don't even have to imagine, because of fucking course they already made it into an episode.