Configuration files also do more than just modify settings, they often (in the form of an "rc file") run a set of commands upon startup (for example, the "rc file" for a shell might instruct the shell to change directories, run certain programs, delete or create files — many things which do not involve modifying variables in the shell itself and so were not in the shell's dotfiles). This convention is borrowed from "runcom files" on the CTSS operating system.
This functionality can and has been extended for programs written in interpreted languages such that the configuration file is actually another program rewriting or extending or customizing the original program; Emacs is the most prominent such example.
The "rc" naming convention of "rc files" was inspired by the "runcom" facility mentioned above and does not stand for "resource configuration", "runtime configuration", or "remote control" as is often wrongly guessed.
"rc" files are traditionally files which end in the "(.)rc" suffix and which contain data and information that is used as configuration information for the associated program. Typically the name of that program is the first part of the rc file's name, with the "(.)rc" suffix being used to indicate the file's purpose, e.g. ".xinitrc", ".vimrc", ".bashrc", "xsane.rc".