I think Cadence is a more suitable Aphrodite, personally.

Pinkie is quite obviously Pan/Dionysos.
 
Rarity might make a good Hera. :)

Twi makes best Athena. <3

Luna is Morpheus.  
Celestia is Helios.  
Faust is Zeus.

Fluttershy could be Pan.

@Carmen Sandiago: Agreed. I believe Twilight Athena is my new patron goddess.
 
@LordAnubis: those seem like fair comparisons (especially when you consider some of Fluttershy’s beast-master attributes). Then again, Celestia and Luna might be more fit to play the roles of Apollo and Artemis (what with the Romans giving those twins dominion over the sun and moon) Pinkie Pie would probably be Dionysus, Spike could be Hephaestus, and Applebloom could be Persephone.
 
@FanOfMostEverything: I believe Rainbow Dash would be best suited to the role of Hermes due to her speed and her love of pranks. Ares might actually be Shining Armor (being Athena’s/ Twilight’s more war-like brother and all). Still unsure of who’d be Zeus, Poseidon, or Hades, but I’m pretty sure Discord would be Kronos.

Ares, Zeus? No way, man, Dash would definitely be Hermes.

Dash would make a good Ares. Or possibly Zeus, given both her job and her status as the fandom’s shipping bicycle.

Amazing chest ahead

Applejack is Demeter  
Fluttershy is Artemis, I guess. Not so much the hunter part, but very much the loner part.

Twilight is best Athena.