The columns at each floor are designed to hold several times the load above them.
As for the factor of safety, the core column cross sections and steel type have been released, we know the weight of the building above the 98th floor of WTC 1 from Gregory Urich's mass analysis, and we can determine cross section of the perimeter columns from Urich's mass anlysis also.
The core cross sectional area at the 98th floor was 2,645 sq. inches and the perimeter 3,682 sq. inches for a total of 6,327 sq. inches. The weight above was 69,303,00 lbs. We also know from the Engineering News Record that the unit stress of both the core columns and perimeter columns was kept the same at each story to avoid differential deflection and floor warpage so the core and perimeter columns at each story had the same stress.
To find the stress divide the total weight above by the cross section of the columns at a particular story. For the 98th floor you get 10,953 psi, and if you look at other stories you will find the column compressive stresses to be approximately 11,000 psi.
The core columns were made from 36,000 and 42,000 psi steel. Divide that by the 11,000 psi stress and you get a minimum of 3.27 factor of safety. This is for compressive rupture. Buckling could occur at about 95% of that so the factor of safety was actually about 3.00 to 1 for the worst case which is buckling.
The perimeter columns were made from 65,000 psi steel at the 98th floor and were stressed to 11,000 psi by gravity loads.