The way it was explained to me was that they can control the speed of the protons as they enter your body. As they approach a certain speed, i.e. slow down, they start to attract electrons to replace the ones stripped from them (good call, bad wording on my part), this causes the surrounding tissue to give up electrons and lose their structure from the atomic level, and the tumor breaks down. They do all sorts of scans and tests to determine the depth the protons need to start doing their work, and where they would "peter out" so to speak, and they build a block of wax infused with a material (can't remember what is was" that regulates the point at which the protons slow down enough to do their work. This is a hollowed out block that has a topographical 3D map, so to speak, of the tumor site, and the proton beam is fed through this block to tailor the shape and depth of the treatment. Obviously some protons go rogue and such and so you get some minor impact to tissues on the way in, and on the way out, but that is drastically reduced compared to the damage caused from the surface with regular radiation treatment.
For proton therapy they have to ensure you are always in the correct alignment, so I got a tiny tattoo behind my ear and on my neck which they use with lasers to line you up. They also made a mold of my body, lying on my back, and made a facemask out of heat-sensitive plastic that got bolted down over my head to align everything. Each treatment took about 15 minutes and I got 5 per week for 8 weeks. The only side effect I noticed was some trouble swallowing due to the proximity of my throat to the treatment zone, and the angle they had to use with the machine to reach the tumor site, but that went away after about 2 weeks and didn't bother me after.
The other cool thing about it is that the facility, at least the treatment center, is about 5 stories under ground. To be able to move the beam and aim it they need an apparatus with a fairly large circumference to be able to guide the beam, since they can't just bend it or reflect it off a mirror or something. So they had a gantry that was huge, and mostly buried underground. If I remember correctly they had 3 treatment gantries tied into the main accelerator.
More info from their site:
https://www.llu.edu/central/info/legacy/chapter5.page
So yeah, 3 rooms with gantries to aim the beam. All in all it was a pretty wild experience to end a year in hell, so to speak.
As a side note, you know one of the worst things about cancer treatment? Boredom.