Travel in Israel/palestine

Is there a direct way using public transport to get from Tsfat to Jerusalem? preferably through the west bank.

Not through the West Bank. To see your options on this and all your other bus queries, look here (search with "include connections").

Is there a direct way using public transport to get from Hebron to Masada

No. There isn't even a road from Hebron to Masada. You have to go via Jerusalem, changing buses there.

the nicest place to swim in the red sea close to Masada?

I assume you mean the Dead Sea. The closest bathing beach to Masada is at Ein Gedi, 17 km. away.

Is there a direct way using public transport to get from Masada to Jaffa?

No. You have to change in Jerusalem. Jaffa is part of Tel Aviv. You can walk from the central bus station in Tel Aviv or take a local bus.

If you need more help on any of this, write back.

It sounds like it might be worthwhile for you to rent a car with a GPS, so that you don't have to waste valuable time waiting for busses.

I imagine the reason the reason the OP asked specifically about public transport is because a renting a car isn't an option.

But if you do rent a car, note that if you drive an Israeli rental car in Hebron (as well as other Palestinian cities) your insurance will not be valid. You are+ allowed to drive along Road 90 (the north-south Jordan Valley road), which is under Israeli control. Also make sure that if you do this, that your GPS will tell you when you are about to enter Palestinian Authority areas. I don't drive myself and have no experience of GPS, but from what I have read, on this forum and elsewhere, there is an +option for this. The most direct way on the map might take you through areas under Palestinian control, where as I said your insurance is not valid.

By far the quickest way from Tzfat to Jerusalem is via Road 6 (a toll road).

And you definitely do not want a car in Jerusalem or Tel Aviv. It will be a liability there, not an asset.

There is an infrequent bus from Tiberias to Jerusalem through the Jordan Valley, so you can make your way for Tzfat to Tiberias and make that connection

#4
Yes, the 961, twice a day at 6:30 a.m. (which you won't get unless you spend the night in Tiberias) and at 18:30 (when it's dark so you won't see anything). The 962 on Road 6 is much more frequent. The only reason to take the 961 would be if you want one of the intermediate stops. You could of course, if you insist on going via the West Bank, change in Beit She'an as well, but that would be pretty pointless.

I have now looked it up for you and I see there are several direct buses a day from Tzfat to Jerusalem. Since there are no stops between Megiddo Junction and a set-down point on the outskirts of Jerusalem, they clearly go via Road No. 6.

Your desire for West Bank buses will be achieved when you go from Hebron to Jerusalem.
Two options, in no particular order:
(a) Palestinian bus to the Damascus Gate of Jerusalem's Old City, no set timetable;
(b) Egged to the Jerusalem central bus station, timetable on website above.

I don't know the fare on the Palestinian bus except that it's cheaper than Egged, but you will then have to cross Jerusalem from the Old City to the central bus station. Either a ride on the light rail for NIS 6.60 or a 40-minute walk. If you take Egged to Jerusalem you'll arrive in the central bus station which is very convenient since that - by an incredible coincidence - is where the bus to Masada leaves from.