It mostly stems from the fact that, like you said, paladins are all about the spell damage.
While not so much as shamans, who get most of their dps from totems, shocks, lighting, lava lash and windfury, and only a little bit from stormstrike and white damage.

Paladins, atm, feel to me like a bit of a broken class.
There is no rotation, no rhyme or reason between their attacks.
They just throw out attack after attack and then wait on what one comes of CD 1st.
"I'm gonna use a weapon strike now!"
"Now I'm gonna make a giant holy hammer come at you from above!"
"Now I'm gonna blast you with a holy-fire spell thing!"
"Now I'm gonna make a big holy tornadoe with some spinning hammers come out of me!"
"Now I'm gonna throw a hammer straight at you!"

You could argue that pallys are the hammer bros., but if you ever dps as one you'll see they feel a lot like they've been cobbled together.

Anyway, back on topic, for armour pen. you really just have to think about how your class deals damage to figure out if its good for you.
Warriors and blood dks get a MASSIVE benefit from APen., simply because 90% of their attacks are physical (Heart strike, Death strike, Mortal strike, auto-attack, Overpower, Slam, Whirlwind etc.) and the only exception is the case of Death coil and Blood boil, which are only really used as filler or aoe attacks.

Frost/Unholy knights rely less on physical attacks then their blood brethren, but still appreciate Armour pen. a great deal.
Obliterate, Scourge strike, Blood strike and auto attack make up a good deal of those two specs damage.
I believe the same rings true for hunters, who use a lot of spell damage in their attacks (Stings, Explosion shot, traps, Black arrow etc.) but also a lot of physical attacks (auto shot, steady shot, silencing shit, aimed shot etc.) in their rotation, making them appreciate arm pen., while not as much as blood dks and warriors, but still quite a lot.

Then you got paladins, bottom of the barrel on the Armour pen. totem pole.
Judgement, Divine storm, SoC/SoV, Consecration and Exorcism receives no benefit from armour pen at all, and these are pretty much 90% of a paladin's dps.