Ok here is coming from someone who knows quite a bit about both Big Boss and Ernesto Guevara.
They are incredibly similar characters in terms of their operations. Infiltration, jungle guerilla warfare (which includes PROCURING WEAPONS ON SITE! Che used American issued M2 Carbines, M1928s, M1911A1s that Batista's men used...) Both are disillusioned, they hate the CIA and the way American emperialsm works and both fight against it. The biggest difference is that Big Boss is his own boss, Che took orders from Fidel Castro. They both have long straight hair with mullets, rough beards, usually wear olive drab military fatigues, wear berets and smoke cigars, but Snake is tall, Che is not. The biggest difference is that Big Boss works for the CIA, realizes the level of corruption, that nationalist ideals are made up by suits to make money while the poor kill each other(In the beginning, he's talking about how he would give his life for his country and the president without a doubt, in the end, he's nearly forced to shake hands with President Johnson.), then he goes on to believe his own set of ideals. Both possess great charisma that inspires individuals around them to join their cause.
This part of Snake's life (Op. Snake Eater) is pretty much parallel to Che's days on the road, where he traveled all over Latin America, and figured something had to be done about the poverty and the corruption, they are different in the ways they are executed, but both start similar and end exactly the same. One of the biggest similarities is that they both operate during the cold war era, 1960s to be exact. Operation Snake Eater takes place in 1964, well after Che and Fidel took power in Cuba but during those years Che was travelling around the world helping, training and fighting amongside rebels (Peace Walker, anyone?). Che is finally captured and executed in Bolivia when the locals are threatened by the military to inform them of the whereabouts of Che's "army". Big Boss is supposed to be killed many times but he always survives(like Che does, before Bolivia) but they get to him eventually. So both are assassinated by the US.
To make things short, yes, Big Boss is pretty much based on Ernesto "Che" Guevara de la serna.
I could provide tens of other similarities but doing your own research is more fun, go and look things up!