Who (and how did they) misunderstood MGS? Kojima isn't exactly subtle.
And considering that Venom isn't even the real Big Boss, and Big Boss was only a true villain in the original Metal Gear, when he had zero backstory and wasn't even cool enough to get more than a fucking placeholder name, it's weird seeing him up there. 2 and 5 pretty much show his goal was to destroy the illuminati as well as take care of war vets who got fucked over by their government. He's only a villain to the shitty fascist governments controlled by The Patriots. He's way more of an anti-hero than an actual villain.
It's like calling Neo from The Matrix a villain because he killed innocent people who were tools of the enemy without their knowledge.