because if you're buying lethality (which used to be flat armor penetration) it affects basic attacks and the old rune system would grant flat armor penetration. this in turn required players to stack early game armor in order to prevent getting 1 shotted by assassins and certain marksmen.
magic damage is typically only found on abilities and special effects to items. It also usually requires some amount of ability power to be dangerous. Champions don't typically start with a base amount of ability power (in fact usually they start with 0 AP and it doesn't scale - unlike AD which does scale as the champion levels). So that means that players have to not only buy the magic penetration, but then also buy AP items AND have abilities that are consistent enough at applying magic damage that they can make decent use of it.
with armor pen all you have to do is auto attack - so increase your attack speed and boom. tough actin tenactin