Ridcully always tells people he's afraid of the Witches because they keep eyeing him lecherously. Ponder says they frighten him because they keep trying to match him up with Magrat.
This, while it is undoubtedly true, is not the whole reason Ridcully and the rest of the wizards really fear Nanny Ogg and Granny Weatherwax.
The truth is that the faculty sees the Witches as competition. They have persuaded them to stay away from Ankh-Morpork for fear of what they might do there.
After all, if people knew what they could do, the Witches would poach all the UU students.