So the more I think about it, the more I'm convinced of...
The Man in Black/Smoke Monster/Fake Locke is the "good" guy. When you take a look at their actions, as well as the actions of the people that follow them, a lot of things don't add up.
I'll try to do this chronologically:
(Quote tags don't mix inside spoiler tags)
"JACOB: I take it you're here because of the ship.
ENEMY: I am. How did they find the Island?
JACOB: You'll have to ask them when they get here.
ENEMY: I don't have to ask. You brought them here. Still trying to prove me wrong, aren't you?
JACOB: You are wrong.
ENEMY: Am I? They come. They fight. They destroy. They corrupt. It always ends the same.
JACOB: It only ends once. Anything that happens before that is just progress.
ENEMY: Do you have any idea how badly I want to kill you?
JACOB: Yes.
ENEMY: One of these days, sooner or later... I'm going to find a loophole, my friend.
JACOB: Well, when you do, I'll be right here."
Clearly, the Others are hostile to anyone from off the island they don't bring in themselves... Remember the 1950's jump? While the time-traveling Losties could prove they weren't in clear contention with the Others, they were very aggressive toward a small group of people. Yes, a nuke had just been brought to the island by a different group, but clearly, the Losties weren't in uniform, and were barely armed, despite being formidable.
Then we've got the Dharma Initiative, the Dharma people weren't exactly "Bad" people, were they? Why would the Others go and kill them, why would they be so hostile? If Jacob believes everything that happens before the end is progress, why not do something to keep from that genocide from occurring? But what happens? The Others kill the people of the Dharma initiative not secretly siding with them, and use everything they brought to the island. Why would they do that? There was no real reason of which we're aware.
Take a look at Sawyer: Parents dead, he shows up at the funeral. Why wait until then? For one matter, he could've spoken to him, and tried to teach him revenge isn't the answer. He could've found him a counselor, or even adopted Sawyer, or find him foster parents. He could have done any number of things to help Sawyer lead a more fulfilling life. What does he do? He gives Sawyer a pen to write his letter, the letter he carries on him until Sawyer finally kills the con-man that caused his troubles.
Flash to Kate, as a child. She steals a lunch box she finds she wants, and as soon as she's caught, Jacob appears and bails her out of it. He tells her not to steal anymore, and it seems like he did something good, right? Except we know Kate's a convict, and in fact, a murderer, once she grows up. What if Kate had been caught? Is it conceivable she'd have learned her lesson, essentially to obey the law, and not become the criminal she was that ruined her life?
I'm not going to lie and say Jacob did something overtly wrong to Jack, when Jack was performing his first surgery. It's possible, though, that Jacob's help and words ("Maybe it just needed a little push.") might have encouraged Jack to live in his father's shadow, or something similar, and we know Jack's life as a surgeon and even as a family man, was tormented by the position his father was in.
Jin and Sun have a difficult scenario to point out. I suppose the best I can say is that he wished them his best, but really, up until the point where they bonded with people on the island, which later split them apart, they grew increasingly miserable together. Jacob's best wishes really weren't worth all that much. This is another scratch, in my opinion.
And then there's Locke: What has Jacob done for Locke? He's sat on a bench when Locke was pushed out of a window, right? Then, when Locke was on the ground, seemingly dead, Jacob walks up, says he's sorry it happened to him, and walks away. How disingenuous is that? He let the man fall out of the building, knowing it would happen, and then apologized for it. Why allow it to happen, exactly? A lot of people believe Jacob brought Locke back to life, but had he, why not fix some of the damage done in such a way that Locke would be able to walk? After all, it can't be that hard, Locke walks immediately upon reaching the island, right? Things don't add up, at this point, I'd say.
A lot of people seem to believe Jacob can heal people. We see him visit Ilana, a new character, and asking for her help. She's in what is essentially a bodycast, and yet, he doesn't heal her. Why not? Again, I don't believe he has any sort of healing ability, and instead, we've misconstrued what we know about Jacob.
Later, we see him two more times. The first is with Sayid and Nadia. Sayid, who has finally found the woman he loves, after spending much of his adult life searching for her, loses her at this time. While Sayid and Jacob are talking about directions, Nadia pauses, and turns toward Sayid, and is sequentially hit by a car, which kills her. She had to turn to speak to Sayid because of Jacob. It's possible Jacob intentionally killed Nadia, which drove Sayid to murder several people out of anger and frustration.
Finally, we see him with Hurley, where it's clear, for once, he doesn't do something to hurt someone. He gives Hurley a guitar case, and suggests that Hurley has a gift, as he see and speak with the dead. This, and possibly the meeting with Jack, are the two "good" things Jacob has done, opposed to the much worse events he's caused.
Oh, and I neglected the time the Oceanic survivors spent on the island.
The Others are very hostile to the survivors of the crash that aren't on specific lists. Why? Why cause so many problems? Couldn't they be helpful, and assist survival to the survivors? I know that Ben was calling the shots, yes, but we also know Jacob, or at least the Jacob that Richard follows, could have issued some sort of command to Richard to change things. Instead, we see kidnapping and killing. We see Locke lead to kill his father, the con man Sawyer had been after. We see Jacob and the Others do virtually nothing when the "bad" people on the freighter attempt to kill everyone. We see someone or something toy with Locke, Claire, and Hurley in "Jacob's Cabin," but we know there's no telling when the circle of ash was broken, so we can't tell if it was Jacob or the "Smoke Monster" causing those illusions.
Essentially, my point is that we've seen very little about Jacob and the MiB. While we know the MiB doesn't like people and wants to kill Jacob, we know that Jacob knows a good deal about things that happened before they happened, and potentially made them worse. We believe Jacob can heal because of Locke and Rose, but really, as far as we know, it really was just the island that healed them, isn't it? We know of the springs, but again, they worked after Jacob was dead, and possibly work better than before. We know he wears white, while the other man wears black, but are we really basing things on the colors people wear? They signify opposition, but not sides. When people play backgammon, does the white side represent the "good" person? Not necessarily.
And so I pose that Jacob has done very little to show he's one of the "good guys." We know he works with Ilana, and her group claimed to be the good guys, but Frank Lapidus was quick to note that most of the people who make such claims don't end up substantiating said claims.
So that leaves us with the Man In Black. We know the Smoke Monster kills, plain and simple. We see it happen from the first episode on. It's clear we don't know why, but we know it does. We know the MiB and the Smoke Monster are almost certainly the same entity, as well. However, we also know that the smoke monster defended everyone at "New Otherton" from the invaders from the freighter, too. We're led to believe that Christian Sheppard is either a apparition of the Smoke Monster, or at least in league with it, and we know Christian helped Michael stop the people on the freighter meant to kill people on the island, as well. There's a few other things that have happened the Smoke Monster is responsible for, but I get the feeling this is long enough. I'll add that the MiB doesn't like people because they do things we, as the audience consider are wrong, and say that we've never seen anything that actually states the goals of either Jacob or the MiB before we learned he "wants to go home." So, essentially, we're siding with Jacob because Ben and Richard have said to side with Jacob, and he's less overt when he causes death or anguish. We're siding against the MiB/Smoke Monster because we plainly see what he does, even though we have seen him do some relative good.
And so, this all said, I think there'll be a twist, where we find Jacob has had some seriously ill intent behind his actions.