A bit of politics

I'm not so sure that I want to get into politics here, but I feel like it's necessary now. I have now been to/through three "settlements" in the West Bank: Me'or Modi'im, Chevron, and the random settlement that our tour guide for the Chevron trip was from (the "through" it the above sentence, as we drove through it on our way back to Jerusalem). I didn't even realize that Me'or Modi'im was beyond the green line until we were coming back and passed through the checkpoint--which, by the way, was nothing. I really don't understand it. If all of this land is Israel, why can't Jews form communities on land that is otherwise uninhabited, no matter where in Israel it is? Why can't Arabs? If Chevron is a part of Israel, why can't Israeli citizens who just happen to be Jews move there if there are houses and/or land for sale? I'm not looking to start a discussion on either side right now; I am just expressing some confusion. I hope to form my own opinions based on my time here before anyone tries to convince me of anything.

That said, this article bothers me. Take a look:

Two policeman and two Muslim worshippers were lightly injured in riots which erupted Sunday morning at the Temple Mount holy site in Jerusalem.

The incident began when a group of tourists entered the Temple Mount compound accompanied by a police force. At a certain stage, some 150 worshippers started gathering around them and calling out towards them.

Some of the worshippers began throwing stones at the group. The police force fired stun grenades in an attempt to gain control of the riot. Two police officers were lightly injured by stones and received medical treatment on the site. They were later evacuated to the Shaare Zedek and Hadassah Ein Kerem hospitals in the capital.

Two worshippers were lightly hurt by the grenades and were evacuated to the al-Maqasid Hospital in east Jerusalem. According to Palestinian sources, 13 people were hurt after inhaling tear gas. Adult worshippers attempted to calm things down, while the group of tourists was removed from the site.

Were the tourists really allowed on the Temple Mount? If not, why were they there? Why were they accompanied by police? What happened before the violence broke out?

And then there's this:

The defense establishment has declared a heightened state of alert across the country ahead of the Jewish holiday of Yom Kippur. On Saturday evening, a closure was imposed on the West Bank until Monday at midnight. Residents will only be allowed to cross into Israel in humanitarian cases.....

Vehicles will not be allowed to pass from east Jerusalem to the western part of the city in order to minimize the friction between Jews and Arabs.

I do have to wonder what time this went into effect last night, since we passed through the checkpoint around 20:30 last night with no line, no hold-up. But what in the world? How is this okay? What's happened in the past that's necessitating this? Did anything happen, or is this another example of Israel not really being one land one country after all?