I would certainly second the Sedona idea. It's hard to go wrong there. I don't know anything spectacular right in and around Flagstaff but there are many things within about an hour's drive. If I recall, Grand Canyon isn't much more than an hour. You can also drive up to Page, then west toward Kanab.
I would suggest getting the book by Laurent Martres, Photographing the Southwest. He has one volume that covers AZ and NM and another that covers southern Utah and Colorado. It has a number of nice hikes and drives that would be great even for the non-photographer.