Again - please keep in mind this is a FIVE-HEADED Mt. Rushmore.
Here are the updated vote tallies...
Doctor Doom: 58
Magneto: 39
Green Goblin: 36
Loki: 32
Red Skull: 28
Ultron: 20
Thanos: 16
Kang: 8
Apocalypse: 5
Mandarin: 4
Doctor Octopus: 4
Bullseye: 2
Mephisto: 1
Juggernaut: 1
Dark Phoenix: 1
Maximus: 1
Sentinel(s): 1
Galactus: (disqualified; seen more as anti-hero/force of nature by most)
*I get it that Magneto is no longer seen as a primary villain, but iconically he still stands the test of time for most of us.