I've only heard 2 credible theories of who killed JonBenet given the totality of the evidence. Either her mother, Patsey, did it in some kind of rage over bedwetting or other issue by JonBenet, or her 9 year old brother, Burke, did it in some kind of sexual assault.
The actions of Ramseys after the crime by the father, John, in deliberately contaminating the crime scene and the mother in attempting to mislead the investigation as kidnapping attempt.. were intended to protect one or other. In any case Patsey is dead, and Burke was beneath the age of legal prosecution at the time of crime.