There are all sorts of circumstances that will set off red lights for either security officials or immigration officials.
If you're flying Israel's national carrier El Al you will definitely have problems going through security . Give yourself plenty of time to be interviewed multiple times by Israeli security agents and prescreening and perhaps having your luggage gone through extra thoroughly. It would be best to bring any documentation that you have IE that you're a foreign correspondent or anything else that would justify your reasons for going.
Remember some of these countries are still in a state of war with Israel. Their fear if you're not a terrorist is that perhaps you mentioned to someone in one of these countries that you were planning to continue on to Israel and that perhaps they gave you a gift to deliver to someone there or perhaps accessed your luggage without you knowing it and placed some sort of explosive device that you don't know anything about. There was a famous case in London that a pregnant British woman had gone through Britain's tight security on Israel bound aircraft only to be interviewed by a El Al security agent who found explosives in her suitcase that were set to detonate in the air . She had a Palestinian boyfriend who preceded her to his parents home in Palestine and she was going there to meet the family that she was going to marry into. Her loving boyfriend put a bomb in her luggage with an altimeter attached to set off an explosion. I know many people go through this feeling personally violated but they can't afford to get this wrong even once.
There is more than one Israeli airline so check it out. If you want an easier flight just take another airline like British Airways, American Airlines, Air France, or Turkish Airlines. In that case you will very likely have a problem entering Israel when you hit Israeli immigration: you will most likely be taken off to the side to be interviewed by Israeli security personnel . If you pass, you get into the country; if you don't pass, you'll be sent back to the country you arrived from. If you passed with a
?, you may be under some surveillance when you are in Israel . But don't worry about it: if they do decide to place you under surveillance you most likely will never know about it. Just go and have a good time .