Later in another lecture at another university, I had to rotate points around a center point again. This time found 3 3x3 matrices on wikipedia, one for each axis. Maybe making at least seemingly a little bit more sense, but I think I never got to the basis of that stuff. Never seen a good visual explanation of this stuff. I ended up implementing the 3 matrices multiplications and checked the 3D coordinates coming out of that in my head by visualizing and thinking hard about whether the coordinates could be correct.
I think visualization is the least of my problems. Most math teaching sucks though, and sometimes it is just the wrong format or not visualized at all, which makes it very hard to understand.