The porous material will not allow larger molecules to pass so these molecules go to the next pore and again they cannot pass. They eventually get to the bottom of the column and exit the column. Remember there is volume inside the column that is not inhabited by the stationary phase which allows for the flow of both the mobile phase and the sample. These larger molecules then find themselves at the bottom of the column whereas smaller molecules have a longer path to travel. Smaller molecules can pass through a pore and then pass through another one. The smaller a molecule is, the greater the chance is that it can fit into a pore which means the longer it spends inside the column.