Rotating something, doesn’t change the size and shape of the thing you rotate; if you rotate a Face in Edit Mode, it stays the same, just in a differnt orientation.
Sometimes you want that, but in a case like this, you don’t want to rotate the top Face of the ‘cube’ (instead, you’ll want to Sheer it, like shown here):

It all depends on the situation and what you are trying to make.
It’s overwhelming in the beginning, but at a certain point it’ll all start to make sense.