Short and sweet.  There's other methods for doing this as well.  Warning:  This isn't an excuse for adding tons of repos.  This simply helps protect the main repos from anything you compile or use rpm to install later.  Safeguards are no excuse for sloppy operations.

$ yum install yum-protectbase
$ cd /etc/yum.repos.d/
nano *insertfilenamehere*.repo

Add protect=1 to any repo that should be protected (each []) and protect=0 to any that don't need to be protected.  In my case, I covered the fedora and livna repos.