Magic and Armor Pen.

champion that deal mixed damage benefits more from magic and armor pen. like Jax, Kayle, teemo

champions that have poor scalings benefits from pen runes (either ap or ad) like sejuani, amumu, leona, mundo

champions that has high scalings benefits more from flat ap/ad more than pen

Who benefits from penetrations?

Everyone really. Armor penetration applies to all the physical damage you do, Magic penetration applies to all the magic damage you do.

Because there are runes that have both. Should i get both ap and ad?

Depends on how far into rune customization you want to go. Generally speaking, every champion is pretty solid with just using an AD page or an AP page.

As for penetration runes: Hybrid Penetration are pretty solid for a wide range of champions in the fighter, tank, and support categories due to either having more mixed damage than anything else or just having magic-damage skills you can't really put AP into scaling, resulting in physical AA's still accounting for a big chunk of your damage.

With penetration runes of any kind: it is worth noting that flat penetrations are actually specifically geared towards dealing with squishy targets and they are hard-countered by armor and magic resistance.

Vs. 30 armor: 30 armor penetration will cause you to deal True Damage. Vs. 300 armor: 30 armor penetration will not.

That's a difference of treating a ~76% damage from physical target as a 100% damage from physical target (exactly a 30% increase in damage dealt), vs. treating a 25% damage from physical target as a ~27% damage from physical target, or a ~8% increase in overall damage.

Considering 30% more damage from AD or AP just increases your overall damage by 30% regardless of what your opponent builds: the DPS drop flat penetrations offer vs. armor or magic resistance causes their gold-to-power ratio to change based on your foe and ultimatly be countered fairly hard by resistance-stacking opponents. All that said: flat magic penetrations are applied after %penetrations, allowing flat magic penetration in particular to remain relevant against beefier targets after building a Void Staff. Due to %armor penetration items largely being in the %bonus armor penetration category with Last Whisper and it's upgrades: you don't have as much synergy on the armor penetration side to make flat armor penetration good for much of anything outside of killing low-armor foes.

Also of note: there's a pretty big difference between armor/magic penetrations being good vs. squishy champions that tend to have 2075 armor and 3052.25 MR vs. Minions that have 0 armor and 0 MR. Penetrations come with a big downside in offering nothing in regards to adding CS potential, relegating a lot of penetration runes to mostly just junglers and supports for an optimal boost in that regard.

Anyways:

Would not recommend penetration runes in top-lane.

Would not recommend penetration runes on a marksman. CSing is way to important, and you have a solid chance of running up against tanky supports that will quickly amass to much armor for them to be of much use.

Penetration runes on mid-lane, especially AP, could help a lot in dealing with MR items through a Void Staff+Sorc Shoes build as well as being decent early vs. a lane opponent and bot-lane targets through roaming.

Hybrid penetrations can be solid on a lot of supports to give them some extra damage early-on.

Penetration runes on junglers can add more ganking potential via more relevant damage in ganks than more clear-based %AS runes, but you're generally sacrificing some clear-speed due to how jungler itemization works.