It is for those reasons, people saw Noah Song's name on the Rule 5 list, and never even stopped to give him even a smidgeon of thought, other than thoughts unrelated to the question of protecting him or not.
If a GM protected every skilled player who had a legitimate shot at making the bigs, someday, the 40 man roster might have 10 guys in single A or looking to get to AA, that year.
Hell, many guys we left unprotected, and who were not selected were invited to ST'ing, something Song would not have been invited to, had he not been selected and made eligible, this winter.
Here was the Rule 5 list:
Enmanuel Valdez (Minor League FA- was added before Rule 5.)
Wilyer Abreu
Dan Altavilla
Angel Bastardo
Brock Bell
Royman Blanco
Brainer Bonaci
Zach Bryant
Cameron Cannon
Brendan Cellucci
Felix Cepeda
Kole Cottam
Wil Dalton
Joe Davis
Osvaldo De La Rosa
Luis De La Rosa
Tyler Dearden
Nick Decker
Jonathan Diaz
Alex Erro
Tyler Esplin
Albert Feliz
Durbin Feltman
Ryan Fernandez
Ryan Fitzgerald
Feleipe Franks
Grant Gambrell
Rio Gomez
Wikelman Gonzalez
Bryan Gonzalez
Devlin Granberg
David Hamilton
Gabriel Jackson
Axel James
Gilberto Jimenez
Christian Koss
Austin Lambright
Dominic LoBrutto
Eduardo Lopez
Bryan Lucas
Naysbel Marcano
Elih Marrero
Chris Murphy
Brendan Nail
Andres Ortuno
Yusniel Padron-Artiles
Eddinson Paulino
Aaron Perry
AJ Politi
Ceddanne Rafaela
Jose Ramirez
Oscar Rangel
Tyreque Reed
Carlos Reyes
Jorge Rodriguez
Giancarlos Santana
Victor Santos
Stephen Scott
Cody Scroggins
Chase Shugart
Nick Sogard
Noah Song
Dylan Spacke
Luis Talavera
Jake Thompson
Freddy Valdez
Michael Valera
Eduardo Vaughan
Jacob Wallace
Brandon Walter
Thaddeus Ward
Alex Zapete
Ryan Zeferjahn
There are 10 guys on this list, not protected or selected that are closer to ML ready than Song likely is.
Some are very skilled and will likely be protected, next year, but since the chances of them being taken this year were about as close to zero as zero itself, they were left unprotected- like every GM does, every year.