Trains. Israel Rail (rail.co.il) has modernized significantly. Fast trains connect Ben Gurion Airport directly to Tel Aviv and Jerusalem. The main coastal line runs between Tel Aviv and Haifa frequently, with trains continuing north toward Nahariya. Tickets are cheap — a Tel Aviv–Jerusalem fare is around 30 NIS. On Shabbat (Friday evening to Saturday evening) trains do not run. Plan around this if you're traveling on weekends.
Buses. Egged operates the national intercity bus network and covers virtually everywhere trains don't reach — the Negev, Galilee towns, the Dead Sea area, and Eilat. Dan runs most buses within and around Tel Aviv. A single bus journey within a city costs around 6 NIS. Buses also stop on Shabbat in most cities, though some Arab towns run services throughout the week.
Shared taxis (sherut). The sherut is an Israeli institution: a shared minibus or large taxi that runs fixed routes at fixed fares, usually slightly more than the bus but faster and running on Shabbat when nothing else does. In Tel Aviv and Jerusalem sheruts run fixed routes through the city center. Very useful on Saturday.
Taxis. Metered taxis are widely available. All licensed taxis have a meter — always insist the driver uses it (in Hebrew: "tefal et ha-moneh, bevakasha"). Tipping is not expected. Apps like Gett and Yango operate across Israel and are often more convenient than flagging a cab.
Car rental. Renting a car opens up the Galilee, the Negev, and smaller towns that buses don't reach easily. Roads are good and signposting is in Hebrew, Arabic, and English. Note that Israeli rental vehicles cannot generally be taken into the West Bank or Jordan, so check the rental terms carefully if you plan to cross borders.
West Bank travel. If you're visiting the West Bank — Bethlehem, Hebron, Ramallah, Jericho, Nablus — note that Palestinian license-plated taxis and buses often provide the most practical connections from the checkpoints. Israeli buses rarely cross. Palestinian-run shared taxis (service taxis) are the standard way to get around within the West Bank.