Yes, in a rollover or side impact, without seat belts, compartmentalization doesn't do much. Those type of impacts are rare, and some other safety features of the bus still help. With a lap belt, the child will stay on the seat and still be protected.
Some school bus safety features:
School bus yellow. It's actually a regulated color. School buses have to be that color, and no other vehicles are allowed to be that color. It's the color that is easiest to see, making buses highly visible and therefore less likely to be hit.
High up. Buses place the passengers high, raising them above the point of impact in all but a few potential scenarios.
Mass. Ever hear "the most lug nuts wins?" The vehicle with more mass generally fares much better in a collision.
A very strong frame. Check this picture out:
http://www.thomasbus.com/bus-models/school/minotour.asp (scroll down).
Now we come to compartmentalization. The seats on a bus are a certain distance apart. They are not allowed to be more than a certain distance so that they back of the seat in front will catch the passenger quickly. At the moment of impact, the bus and passenger are moving at the same speed in the same direction. During the impact, the front crumple zone does its thing, gradually slowing the bus. The passenger keeps moving at pre-crash speed until the passenger impacts the back of the seat in front. Because the seats are close together, the bus has only slowed a little bit in the time it takes for the passenger to impact. If the space was too large, then the bus would slow down more and the passenger would hit the seat a lot harder. Those seats are padded and designed to give a certain amount to absorb crash force.
The body of the bus is not actually rigidly attached to the frame of the bus. This also lets some of the energy dissipate. I thought it was really cool when I learned about it in tech class. The body basically sits on these two long rails that run the length of the bus. The body is held on with a few U-bolts, so it's attached but not. In a frontal impact, the body will slide forward on those rails.
Then there's just plain statistics. Kids are eight times more likely to be killed riding to/from school in their parents' vehicle than on the bus. Kids are more likely to be killed between their house and getting on the bus (walking to and waiting at the bus stop) than they are on the bus. School buses are just so very, very safe.
