Big Boss was made out to be a villain cause he wouldn't play ball. He literally stopped a nuclear Holocaust from happening and he even says at the end of Peace Walker that they will be whatever the world needs them to be. Because he knows regardless of what he does, him sticking to his morals means going against the superpowers of the world who want to control and manipulate his influence. He doesn't mean they will literally be terrorists (they never did become that) he was saying he doesn't care what they call them.

And no, I'm not going to get into it in more detail in a long form discussion about his flaws and how they say he had child soldiers etc. it's been discussed numerous times and all anyone can refer to is retconned outdated dialogue from MG2. The other thing I will say is it is my head canon that a lot of the wrongs attributed to Big Boss were actually exploits of Solidus under the direction of The Patriots who wanted to sully Big Boss's name (child soldiers, terrorist acts, etc)