Visiting Bethlehem and Masada from Jerusalem

I would suggest a guide.
Bethlehem is less than 10 miles south of the Jerusalem city center, but is under the control of the Palestinian National Authority.
Masada is about 60 miles southeast of Jerusalem through the desert. I believe it's correct to say Masada is in Israel, although in 1990 when I visited (and I assume this is still the case) it was necessary to go through Palestinian territory in order to get to Masada from Jerusalem.

So I would say you would want to carefully research these issues if you are thinking about trying to do it on your own. I don't know the current security procedures for visiting either place, since my last visit was 1990.

Being on tours in these areas might make a lot of sense. It's not like doing it yourself in western Europe.

When I went to Masada in about 1990, our guide was armed with an automatic assault rifle.

Some tours to Masada include one or more of the following, all of which are interesting: Qumran, Ein Gedi, Jericho. Each of these can be fascinating, depending upon your interests and those of your group.

I was familiar with the Masada story and what I was seeing and my tour did not include a guide on top. But some people might benefit from having a guide on top.

You mention continuing on to Tel Avis, Haifa, and Tiberias.
May I suggest that you try to make time to stop for a couple of hours in Nazerath on your way from Haifa to Tiberias. And continue north of Tiverius and on to the top or north of the Sea of Galilee, to see Capernam (Kefar Nahum locally), and Safed (prounced Zfaht locally) areas north of Tiberius.

Bethlehem is an easy 1/2 day trip from Jerusalem. You can get buses or take a taxi (it's a short ride - maybe 3 miles, take a taxi!) from East Jerusalem (near Damascus Gate, I think). Unless there's a special alert or a holiday, going through the checkpoint should be routine not take long. I really don't think a guide will help you go more quickly. The delays, if any, would be on your return to Jerusalem. Note that on April 21-23 Israel will be observing Memorial Day and celebrating Independence Day. These are dates that, if you are here, you should plan something else.

The best plan for Masada, based on your itinerary, would be to rent a car when you leave Jerusalem, go to the Dead Sea (there's much more than Masada there) and then drive straight north to Tiberias. The only caveat is that the drive should be made in daylight.

While a good guide can enhance a visit to almost anywhere, if you usually manage without them, you can certainly do so here. What you want to see in Bethlehem is around Manger Square. There will undoubtedly be locals offering to give you guided tours, which you can politely refuse if you like. Masada is a well-developed site, there's an introductory movie and a good audio guide. If you want to do more at the Dead Sea - spa, mud, float, Ein Gedi Nature Reserve, Qumran Park (where the Dead Sea scrolls were found), you should plan to spend a night at the Dead Sea. It's about 2.5 hours to drive from the center of Jerusalem to Masada, and more if there's traffic. From Masada to Tiberias is about 2.5 hours drive - passing Ein Gedi and Qumran on the way. All of these roads are under Israeli control. You will go through one or two checkpoints, but they are typically perfunctory and most vehicles are not even stopped.

If you have time, I would suggest a visit to Banias nature preserve. It's at the base of Mount Herman, near the Golan Heights, and is one of the most beautiful places I've ever visited; you might want to check some photos on the Internet. In addition, it's the site of Caesarea Philippi, with Roman ruins nearby.