Root - administrative access to system, so you can possibly change system/delete system files and settings (and if you don't know what are you doing, you can also screw up the phone). It also allows user to bypass certain security measures, therefore it can be seen as possible danger by antivirus programs.
Don't worry about this, anyway, antivirus is not needed in Android, as long as you read the permissions and don't download pirated programs from suspect sites.