Simply put, a rootkit if well made is undetectable.
And your antivirus or other scanner will miss this if your antivirus or such is not programmed to look for it.
It's that simple. Antivirus scanners only know what threats they know. There are some thoughts about heuristics and more, but a good rootkit is going to be very hard to find.
Example at http://asia.cnet.com/ciq-rootkit-likely-not-present-on-handsets-outside-the-us-62212329.htm
Sorry if this doesn't explain it well.