Whilst it was very well done and an excellent attempt by them to tell the story of the family's treatment in the media and how badly the police messed up the investigation (which they did), I think they skipped over several key details in the crime:
1) the ransom letter was written in the house, they found the sample of it on the other pages of the pad by the telephone - who takes the time to sneak into a house, kidnap/abuse/kill a child and then write three drafts of a ransom letter whilst the rest of the family sneaks upstairs
2) everything used in the murder of JonBenet was inside the house - nothing was brought. This is usually a large indicator someone inside the house did it or a very disorganised killer (and if the killer was so disorganised why did the others in the house not wake up). They did not make this point.
3) they did mention this in episode one, but the Ramsay's never spoke to the police and neither did Burke. They hired lawyers and a media team, but never spoke to the police. This is what incited police and media suspicion. Why didn't they just give an interview with their very well paid lawyers sitting right there telling them to 'shut up' when needed.
There are too many elements of this story to safely rule out the family. It's tragic what happened to JonBenet and the discussion in the press about the sexual assault with little basis (the evidence found in the autopsy can has several explanations, one of which is potential assault) must have been awful. But the documentary has essentially let the family off the hook without actually delving into key details of the crime that suggest it was someone inside the house.