It seems that the norm is to (fast-) fill fuel and oxidiser tanks from the bottom. For example, on this drawing of the Saturn S-IC stage you can see the LOX and RP-1 fill valves at the bottom of the respective tanks (hard to read - click through to see higher-resolution images; the fill valves are near the AB and CD plane markers):
(source: Mike Jetzer/heroicrelics.org - higher resolution images available)
This answer related to STS also shows the STS External Tank to be filled from the bottom.
Naively, I would think that filling from the top is much easier, as you don't have to fight the pressure of the propellant already in the tank, either with a pump or by putting the supply tank higher than the target tank (communicating vessels).
What is the motivation to fill the tanks from the bottom?