Como é frequentemente o caso com termos obscuros, o Arquivo Jargon tem uma resposta :
[Unix: from runcom files on the CTSS system 1962-63, via the startup script /etc/rc] Script file containing startup instructions for an application program (or an entire operating system), usually a text file containing commands of the sort that might have been invoked manually once the system was running but are to be executed automatically each time the system starts up.
Assim, parece que a parte "rc" significa "runcom", que, acredito, pode ser expandida para "executar comandos". Na verdade, é exatamente isso que o arquivo contém, comandos que o bash deve executar.