We've been going to and travelling around Egypt for a number of years. By Egypt - I mean Cairo, Luxor and Aswan.
In around 8 holidays there, we've only ever take 2 organised excursions with a tour operator representative and that was only because it was convenient to do so.
One of these was the cruise to Denderah temple and the other was a half day tour around Cairo. From Cairo, we arranged our own trip to Alexandria by train (a cost of around 3 Gbp per person as opposed to a taxi indicated necessary by our rep at a cost of 25 Gbp per person).
Mostly, we've been based in Luxor for a couple of weeks and then done all our West Bank excursions under our own steam, taking taxi's etc. We also went to Hurghada on an overnight stay in a hotel including snorkelling and have taken several overnight train journeys to Cairo.
Our last holiday was in May 2007 but this time we went from our new home location of Cyprus - again, all organised by ourselves. We used Memphistours to reserve an overnight train from Luxor back to Cairo as we were limited on time in Luxor to be able to ensure we could get the seats and we were flying back to Cyprus from Cairo and they also reserved our 3 night Nile cruise from Aswan to Luxor. They sent a rep to our Aswan hotel with the tickets, the morning after we arrived as agreed and no hassle at all. We would definitely use them again as well as recommend them to anyone else. We paid a 25% deposit and the rest when we collected the tickets from the rep.
Maybe there has to be some consideration regarding your holiday insurance, but your tour operator cannot be on call to get you around your resort and chosen destination 24hrs a day, nor can they expect you to not go anywhere other than on their excursions or not use public transport etc. However, you should consider such things as balloon flights, boat trips etc may not be covered on your insurance should you have an accident if you take these not escorted by your tour op.
I would suggest it's better to take an independent insurance policy in any event rather than being tied with the one offered by the tour operator.
CwB