The first lecture was using a 4x4 matrix because you can use it for a more general set of transformations, including affine transforms (think: translating an object by moving it in a particular direction).
Since you can combine a series of matrix multiplications by just pre-multiplying the matrix, this sets you up for doing a very efficient "move, scale, rotate" of an object using a single matrix multiplication of that pre-calculated 4x4 matrix.
If you just want to, e.g., scale and rotate the object, a 3x3 matrix suffices. Sounds like your first lecture jumped way too fast to the "here's the fully general version of this", which is much harder for building intuition for.
Sorry you had a bad intro to this stuff. It's actually kinda cool when explained well. I think they probably should have started by showing how you can use a matrix for scaling:
[[2, 0, 0],
[0, 1.5, 0],
[0, 0, 1]]
for example, will grow an object by 2x in the x dimension, 1.5x in the y dimension, and keep it unchanged in the z dimension. (You'll note that it follows the pattern of the identity matrix). The derivation of the rotation matrix is probably best first derived for 2d; the wikipedia article has a decentish explanation: