At Masada, there is an attended parking lot, and at Qumran, the lot is very close to the main building. I would not hesitate to park there and leave luggage in the car, but recommend that you cover it with beach towels as an extra precaution.
Your luggage should be safe in your car - obviously, take the necessary precautions, cover with a towel or something like that, try to have everything in a closed trunk - but as Moti pointed out the Dead Sea and Masada are in the opposite direction from Jerusalem than Tel Aviv - so your plan has a glitch in it.
Personally covering luggage with a towel is not covering it. It is easy to see what is under the towel so you need a closed trunk. As said--Dead Sea is not on the way to Tel Aviv. While it is slightly out of the way to return to Jerusalem I would consider it, thereby leaving luggage in Jerusalem. What are your days looking like? Maybe we could help you rework your itinerary.
Leaving your luggage in the car is a problem all over the world. I am always hesitant to leave stuff in the car in many countries like: Italy, Spain, Greece, France and, yes, even in the good old USA. Israel is no worse and perhaps even better than other countries.
Your main problem is, as Moti wrote you, that your route doesn't make any sense at all. But if you insist on doing all this on your "way" to Tel Aviv, I would follow rdglady's advise: Leave your luggage in Jerusalem and pick it from there at the end of the day on your way to Tel Aviv. It will put your mind at ease.Edited: 19 July 2010, 06:46
I have left luggage in my car many places including Israel. I agree that you have to put it in the trunk and rent a car with a trunk not a hatchback. Also don't park and then get something out of your luggage in the trunk. In otherwords don't advertise that there is luggage in the trunk. Don't forget it does get very hot in Israel. So if you are not parked in the shade make sure there is no medicine in you luggage and anything that can run or go bad.
A large number of smaller rental vehicles in Israel are hatchbacks. They all have "screens" and luggage is just as hidden as it is in a regular trunk. The problem is visibiity. A towel doesn't "hide" luggage the same way as a trunk or hatchback screen.
As an aside for over 20 years I owned a hatchback vehicle(s) in the US. I loved it and felt very confident leaving all kinds of stuff in the "trunk" It cant be seen.
We parked out sedan car with luggage in the trunk at the free parking lot at Ein Gedi and went for a float in the sea. We were gone about 30-40 minutes, and had no problem. It was out in the open, and anyone could see if someone tried to open the trunk.
From Masada, it is slightly easier to get to Tel Aviv by driving through Jerusalem than via Beer Sheva. It takes about the same amount of time.
Since you lose nothing by returning thru Jerusalem, it should only take you a few minutes to detour off the main road to pick up your luggage and avoid the potential problems of having luggage in your car all day. Personally I don't leave anything in my car that can be seen from the outside, including in the parking lot of my building. Having something covered by a towel or blanket is no different than having a closed suitcase, it's still having something enticing in the car. Many people do and nothing happens. But it does happen to some people and you don't want to be among the unlucky ones.
Thanks for all your replies. Sounds like it's best to drive back to Jerusalem before heading to Tel Aviv. And thanks, Sailingdays. I didn't consider how hot the trunk would get! I had a bottle of wine explode once because of the heat in a closed car. Points well taken.