I visited Israel with a Christian group and through Pilgrim Tours in 2004 (see their web site). It was a great experience and well worth it. We arrived in the area at the time of the funeral for Arafat and tensions were high, but we were all kept clear of bad areas. Israel values tourists and we were well guarded and guided ---they have reportedly never had real troubles with tourist groups. We saw all the main sites and places, beside museums and government buildings, the real sepulcher of Jesus, and the Temple mount, etc. Food and lodging was very good, and we even got to stay one night in a Kibbutz. We traveled in a big tourist bus from the sea north across and south into desert and the famous Masada site.
Our guide was a Christian Jew of the Naphtali tribe and well versed on the history of the country and religion, and he was very helpful. It was most educational and scenic, in towns, historic places, and countryside for about a week. It would be nice to go again.