To begin to answer your question, I must note that skim milk also undergoes homogenization before it is sold. There are two processes here to discuss: homogenization and separation.
If left to sit, the fat molecules in milk will stick together and separate out from the rest of the milk. These fat molecules eventually rise to the top of the milk as the cream. Because consumers like a consistent texture to their milk without any separation, milk goes through a process called homogenization. As milk is homogenized, it is forced through tiny holes at very high pressure. This breaks the fat molecules down to a small enough size that they will no longer separate out and create cream. Homogenization is done to all types of milk (whole milk, reduced-fat milk, and skim milk) to prevent separation.
To make skim milk, the fat is separated from the milk, usually by using a centrifugal milk separator. This separator spins the milk at very high speeds, and the fat is collected and used for making products such as butter. Skim milk is left with about 1% milk fat, which is why it still needs to be homogenized to break those fat molecules down so they won't separate out. Because of this, separation usually occurs before homogenization.