What are the negatives when comparing this trip with one arranged by a travel agency or travel service?

I think there are several possible answers:

1. It is a physically demanding trip.  We start early and go hard. Jerusalem and its environs involve constant walking up and down steps or hills.  Most tour groups avoid much of this by busing from site to site. Generally we won’t be doing so.  We will walk so that we can see all the sites that cannot be reached by a bus. If you are not in excellent health and excellent physical shape, do not ask to join this tour.  (No, you don’t have to be an Olympian. I have always had at least one traveler over 70 and my mother went with us in 2000 when she was 75 years old and bowed out of only one activity in all of Israel—an activity that was more strenuous than anything currently included on my trips.)  Our first full day in Israel is the hardest. We will put in miles of walking on that day. One of the benefits of keeping us moving during the first day is that you will do much better at adjusting to the time than you would if we went to a museum and you had to stand still and listen to me talk. You will be expected to stay up with the group.
2. Time to casually shop or take photographs is limited.  We generally do not stop at souvenir stores. (Most for-profit tours have such stops because commissions for the tour company for anything the tourists purchase are typically 15%-30%.) There will be a time for independent shopping but never when our group is in the middle of a tour. You will be able to take lots of pictures but never to the point where it holds up the group.
3. The unexpected may occur.  Because this is cheap travel with no free days included in the itinerary (though we do have some free-time hours) sickness or failing to catch a bus will mean sites are missed.  I make arrangements with the drivers when they are used.  If one were not to show up on time, it would definitely impact us.  We have never had a bus not show up, but it could happen.
4. Accommodations are clean, safe and ideally located, but our price sometimes involves group dorms with separate areas for men and women.  (Private rooms are available, but you would have to pay the difference.) Our accommodations do not include the five-star rooms included on some tours. They are very basic but ideal for our purposes.  
5. Most meals are prepared by our personal chef.   (She will require some assistance from you.)  You will probably eat as well as you ever have.  Yes, I know you don’t believe it, and for you Francophiles it probably isn’t true, but I do believe the food we fix is really good and healthy.  
6.  When in Israel, we drive rental cars from Budget. Rental cars allow us to move around the country quickly and without great expense, but they are small cars, not stretch limousines.
7.  Our price may have to be increased slightly when the trip is over if prices were to increase much. With oil’s rise in 2011 (we paid $8.50 per gallon for gas in Israel), we almost exceeded our budget. I have never had to ask for additional money but almost had to do so in 2011. (We ended with only $3 per person left in our Group 1 account.) I budgeted $10.00 per gallon for gas for 2013. Gas probably cost that much earlier this year, but with the recent fall in oil, I am hoping for more moderate gas prices when we arrive. Of course, there is no way to know what the price will be this far in advance. 
8. The amount of luggage you will be allowed is more limited than you would be permitted on other tours.  One 15”x 22”x 9” suitcase and a school-type backpack or a large backpack and a school-type backpack are all anyone is allowed—two pieces of luggage. Of course, my family did an 8 1/2-week Middle East trip in 1996 with less than these limits without ever feeling a need for more room.