I got to say that i can´t understand why you ppl have so much doubt on who's the bad Guy question!!!!
1º- White Rock vs Black rock, In all the beliefs the black is always the evil and the white allways represents good.
2º- Second and in my opinion the most obvious, the "Man in Black" Kills ppl, inocent ppl! Jacob never interferes! The ritters are shouting... the "man in black" is a bad guy! Now, why did i said A bad guy and not THE bad guy?
Because one might say that Jacob is also bad. How?
Jacob is responsable for all the crashes on the island, and those same crashes kills ppl on the process. So you can reach to the conclusion that Jacob also kills ppl, and there for Jacob is also a bad guy.