1. Since you took the route from Jordan, when you reached the border and you gave them your pasport was it your amercan passport or any other? Because Israel does not have relations with any muslm country accept turkey. Did you take visa from the israeli consulate. I also heard that they do not allow entry for someone who is below the age of 40. If thats the case then it would be very hard to get in to Jerusalem.
Bismillah. The State of Israel insists that Jerusalem is its capital, and so to visit Jerusalem the Israelis will insist that you have their permission. You can apply for that permission from the Israeli Embassy/Consulate in your country of residence, or you might be able to get permission at the border -- but that depends on your nationality(ies).
If you are Muslim, your experience might be like mine. I met at least 15 non-Muslim travelers at the border during the two days it took for me to cross. The Americans seemed to cross easily -- at least they did not have to sit in the waiting area. The Europeans and Asians (Koreans) I met at the border were all forced to wait for at least several hours, but in the case of the Europeans, each of them had visited Syria or expressed their intention to do so.
Alhamdolillah (ala kulli haal), I only have an American passport. US-Israeli relations are such that Americans visiting Israel normally can seek permission at the border. So, that's what I did. I'm under 40, and I got in.
I did not have the problem that, for example, a Pakistani citizen would have. Pakistani friends and relatives assure me that Pakistan-Israeli relations are such that a Pakistani would be punished by Pakistan for entering Israel, and Israel might not even grant a Pakistani permission to enter even if he applied to an Israeli embassy in a third country.
I do not have a lot of information on travel requirements for people from other countries, but my understanding is that Jordanians and perhaps Egyptians are able to travel to Israel.
Here is a very resource-and-information-packed web page that I never visited before today: http://travel.state.gov/travel/cis_pa_tw/cis/cis_1064.html Despite that ringing endorsement, I really do recommend that you read that page.
If it makes you feel better, I did visit this page: http://www.israelemb.org/consular_Visa.html , and if you want to go to Jerusalem you should visit it, too.
(Added after initial post)
Although I briefly mention the fact here, since this question was about visas, it bears repeating: if you ask the Israelis nicely, they might not stamp your passport on entry. A lot of people worry about this, and not just Muslims. Every time someone was asked about the stamp in front of me, each person replied that they did not want the stamp in the passport -- Muslims and non-Muslims alike.
As far as I know, the decision is entirely up to the Israelis. I was asked no fewer than three separate times whether I would permit the stamp. Each time I asked them to stamp a separate piece of paper. In the end, I was given a small piece of paper indicating that I had been given permission to enter Israel, and the immigration officer stamped it with my visa.
A guard at the end of the hall, asked for the piece of paper, tore it to show it had been used, and then threw it in a trash can when I did not ask for it. Apparently, I was supposed to ask for it. So you should do so if the guard does not hand it to you on her own. Because that paper was my only proof of permission to enter Jerusalem. Not having that proof made me very hesitant to travel far from al Aqsa, so alhamdolillah, it worked well for me.
No mark was put in my passport.
But my passport and luggage did have stickers placed on them by the Israelis to track them while I was at the border. I removed all of them by the time I returned to Jordan.
