Look for a tour that doesn't start too early each morning. Make sure the hotels you stay at have swimming pools and certainly add on a few days at the Red Sea to your itinerary. A long cruise down the Nile isn't ideal if you're traveling with young children since there's not much to do other than visit ancient sites. A trip to Luxor and then on to the Red sea is a more family-friendly way to go. Try to avoid the very hot summer months especially if you plan to go to Luxor and/or the Desert.
See Tour Egypt's article about bringing your children to Egypt for more information.
Recommended Egypt Family Tours:
Thomson Family Adventure - 10 days in Egypt includes Cairo, the Red Sea and Luxor. This trip departs from the US.
Abercrombie and Kent - A 10 day family holiday which includes Cairo, Abu Simbel, and Luxor. The Nile cruise has a children's activities coordinator on board.
Adventures by Disney - a 9 Day family-friendly itinerary with expert guides leading your group and enthralling kids with hands on activities and lots of personal attention. Includes Cairo, a Nile cruise and the beaches of Sharm el-Sheikh.
Responsible Travel's Handpicked Family Vacations - Vacations include camel rides in the desert, one week and two week family-friendly itineraries, farm-stays, dolphin watching and more.