Security or Other Reasons?

I wanted to point out this clip I saw on the website of one of the large Israeli newspapers. I'm not as concerned with this specific incident as I am with the principle of things.

When the Israeli government does things to protect its citizens I think that that's absolutely fair (and necessary). When they do things that are extraneous to this, it's hard to watch. When I fly out of Tel Aviv and go through 2 hours of being asked questions and having my luggage looked through (and I'm not exaggerating, sometimes it is 120 minutes) that's ok, because they want to make sure no one is going to harm people on the plane. When they do things like the clip talks about, or won't let people travel from one place to another to farm a field or see Jerusalem, those are the things that I think are unjust and ultimately hurt Israel as a country. What purpose is served by not allowing them into Jerusalem? These are just a few of the people we know from Bethlehem that aren't allowed to pass through the checkpoint and go to Jerusalem. Do you think they're a security risk to the state of Israel? I don't, but maybe I don't know enough yet.
Sure, search their cars or make sure they aren't bringing knives, guns, or explosives into Jerusalem (terrorists have used children to smuggle explosives in the past here; just as an aside, if you have the time to read this article, make sure you read the whole thing; it brings up the whole issue of lack of credibility and distrust on both sides and how that affects the situation, and both sides distort facts on a regular basis), but to completely deny them entry at all seems to be serving an entirely different purpose than ensuring the safety and security of Israeli citizens. What do you think?