Excellant points Old Broad, and add to those, if Burke had been sexually abusing JBR in the past, I think JBR would have mentioned something "wasn't right" to her mother, or someone else. While I totally believe Burke was jealous of all the attention JonBenet was receiving, I don't believe he was involved with her that night in that fashion. JBR was by all reports a strong willed little girl, and I'm certain not only would she have told on Burke, but in the very least, threatened to "tell mom" at the very first instance of his abusing her.
Edited to add: while writing this post, I thought of something. It's reported that Burke was pretending to sleep that morning when his parents checked on him. Maybe, just maybe, he heard a commotion the night before between either parents and JBR (screaming, yelling if they did this) and was scared. You know, how when kids are scared of the Boogey man, they lay there and pull the covers over their heads? It's also strange he didn't ask for further exmplations the next morning when they sent him to neighbours and JBR wansn't around, and a trip was planned. It sounds to me like he definately heard something that scared him from persuing any matters from the night before. Heck, any kid would ask, where's JonBenet, what's happened, why aren't we going, what's going on? The Rams apparently didn't tell him anything. Burke KNEW something very, very bad happened during the night between JBR and his parents and knew better to ask any questions out of fear he may experience harm, jmo