Yea... as far as I've understood, these are the most widely spread meanings of the words: a "scanner" is a program that scans for Internet computers vulnerable to certain security bugs, and a "rooter" is a program that actually seizes control of such a machine, making use of such vulnerabilities. I've also seen the people who make use of these kind of tools being called "scanners".
These terms are mostly being used in the warez (illegal file sharing) scene, where most victim hosts would be Windows machines, but apparently the act of becoming administrator remotely is still called "rooting"...
