Buses , mini vans , trains are the most commonly used means of transport. Monit Sherut are mini vans that are faster than the normal buses and the advantage is that it runs during shabbat too. They not only stop at official bus stops but also at other places. The drivers usually wait until the van is full and at times it can keep you waiting.
Arkia , Israir ,Elal airlines provide domestic services and the prices provided by Elal airlines is quite cheaper when compared to the other two airlines. It can easily cost around 30 USD or more for one way trip. Domestic air service is applicable to cities which include Tel Aviv , Jerusalem , Eilat , Galilee , Negev , Nazareth and Dead sea.
Official railways website - http://www.rail.co.il/EN/Pages/HomePage.aspx Israel railways is modernized and there are several rail routes that connects inter cities. Tel Aviv has 4 train stations and Haifa has 6 train stations. The intercity lines are Nahariya to Beer Sheva via Haifa, Tel Aviv and Ben Gurion airport ; Tel Aviv to Binyamina, Ashkelon, Kfar Sava, Rishon LeZion, Modiin and Bet Shemesh. There are also lines between Bet Shemesh and Jerusalem, and between Beer Sheva and Dimona. Train fares are equal to twice the bus fares and it is considered quite expensive. Nevertheless , it provides great comfort , speed and safety. Train fares are cheaper than taxi fares .
Bus.gov.il and Bus.co.il are the official websites that can help you to plan your schedule. Buses are very cheap and reliable means of transport. However , it is generally difficult for tourists to figure out the route and timings . It is recommended to use apps like google maps or Moovit which can help hugely. Taxis are also common. It is better to prefix a price or strictly instruct the moneh ( meter in Hebrew ) to be switched on else the drivers will try to rip you off by charging more and at times they can be very rude. Taxis which serve from airport usually have fixed fares and these taxis belong to Hader Taci company . You will have to pay VAT if you dont provide Visa for car rentals. Also, the Israeli government requires expensive insurance on rental cars that can cost up to USD 20 per day. Renting car can be a better option if you plan to visit many places and it will cost around USD 200 a day which includes guide .