Here is anexample of how TapRooT can be used, from the Flight Safety Foundation
http://flightsafety.org/files/TapRooT_application.pdf
To me the crux of any RCA has to be understanding the Problem Statement or Definition to start with.
I haven't studied Colgan in depth, but my understanding of the cause was that the pilot made an incorrect control input in response to the incipient stall warning. That was the cause and all the other factors were 'contributing'.