Several theories have been put forth since LA X about the origin of the ATL. It's an epilogue, it's a prologue, it's simply the consequences of the actions of the time travelers in 1977. The last of those has become particularly popular again since Daniel and Desmond's conversation in Happily Ever After. It seems the writers are pointing us in the direction of a simple answer - the characters mucked around in the timeline and caused an alternate one to form. Easy peasy, right? Well, as easy as Lost gets, anyway.
But there are problems with that supposition. I'm gonna focus on one, since it's still gonna be fresh in people's mind: How does Pierre Chang still have his arm if it was damaged before Jughead could have exploded? Well that's an easy solution too, some have said. Since the plane didn't crash, there were no characters time traveling to the 50s and the 70s and so they retroactively erased their own actions and the Incident (and other events their time traveling caused) didn't happen, or didn't happen in the same manner, at least. Still pretty simple and straightforward, right?
But Dr. Chang is still a problem. He doesn't have any kind of handicap in the alt, (except looking pretty good for a guy who's gotta be 60 or 70. Note to the Lost makeup department- a little gray hair doesn't really make a guy look 30 years older.) but he still does in the original timeline. That may not seem like a problem when you think about it, but it may imply that the timeline "split" isn't as simple as Jack & the bunch retconning themselves.
Because Dr. Chang is missing his arm and references the Incident in the Swan video in the original timeline, we can assume that a) an Incident of some kind did happen in the OTL and b) Dr. Chang lost his arm at some point in that timeline. For what we saw in The Incident (the episode, not the event) to be the explanation for those things, then the events of The Incident have to be what always happened. As Daniel said, what happened, happened.
To summarize- For Dr. Chang to still be missing his arm in the Swan video, the time traveling Losties interfering with the drilling at the Swan site had to have always happened. They always crashed on the island in 2004, left the island, came back in 2007, time traveled to 1977, convinced Dr. Chang to go to the Swan site, and then themselves caused the Incident, which caused Dr. Chang's arm to be amputated by the time he filmed the Swan video, which they themselves watched in 2004 after their plane crashed as a direct consequence of the Incident. Still following? This chain of events is a time loop, but not a paradox according to the show's rule of what happened, happened.
(Side note - in real life that's called an ontological paradox, also commonly known as the Terminator Paradox, referencing how John Connor sent his own father back in time to impregnate his own mother, ensuring his own birth and allowing himself to send his father back in time. The loop had to have started somewhere and causes a chicken and egg style problem, hence the paradox.)
So if they always went back in time and caused the Incident, that means Jughead was always there with the time travelers and either did or did not explode. (We still don't know.) By the show's established rules of time travel, there's only one timeline that is immutable. (What happened, happened.) The evidence of Dr. Chang's arm supports this.
Jughead can't have both changed and not changed the timeline at the same time. It was either always there and always went off, or it wasn't. Dr. Chang's arm implies the first. Therefore, "Jughead caused the ATL by causing the Losties to never time travel" can't be the whole answer, as that leaves a paradox. Did it change the timeline or didn't it? Since our most direct evidence is Dr. Chang's arm, it looks like it never changed the timeline at all.
That leaves 3 explanations - Jughead, for some reason, created a Schrodinger's Cat situation where both timelines exist because the bomb both did and did not go off. But if "what happened, happened" with the Incident, then that must have been happening at each iteration of the time loop that the Losties themselves caused, which is kinda weird and kinda complex, but hey, so is time travel, unless this particular iteration was in some way special. (Remember, if we're to acknowledge that Dr. Chang's arm was missing in 1980 [as observed by Jack and Locke in 2004] because of Daniel convincing him to go to the Swan site in 1977 and that Jack & Co. were there when the Incident occurred, then that had to have always happened, which means the Swan was always built as a result and the plane always crashed because Desmond was out horsing around instead of pushing the button. Shame on him.)
Or, quite possibly, ATL is unrelated to Jughead and the whole thing is one big red herring. This is probably the easiest to explain, depending on how they decide to tackle it.
Or, Dr. Chang lost his arm in the OTL some other way and him losing it in the Incident was some kind of course correction, which also fixes the ontological paradox. But that'd introduce yet another different timeline and complicate things further, so I think it's unlikely from a writing standpoint. (And yes, I know that he somehow has it back in the Pearl film, but I think that's been acknowledged as a continuity error.)