explanation for the last movie really doesn't make any sense. Star Trek has always been a series where changing the past changes the future. To suddenly say that Nero and Spock going back in time and changing the future created an alternate reality doesn't fit with the show. If that were the case then there was no reason for the Enterprise-E to go back in time and stop the borg, because all the borg would have done was create an alternate reality.
If you're going to use an alternate universe approach then that's fine. You could say the two storylines take place in alternate universes and don't affect each other. The problem with that is the "prime" storyline is following the same events. Hobus goes supernova, Spock tries to stop it with red matter and travels through the black hole with Nero. So that would mean he is in the past in this reality as well, so the timeline should be changed. If changes in the timeline are suddenly not possible then the storylines for dozens and episodes, books and even some of the movies are irrelevant.
It actually makes sense if you bear in mind that after changing the past, when they jump back to the future, they remain in an alternate timeline more-or-less to their preference. It doesn't change the fact that the original timeline continues to progress. Take ST4 for example: in the "original" timeline, all life on Earth is wiped out by the probe. The timeline is modified by the end, and we progress on in an alternate timeline wherein Earth is saved. The inhabitants of that universe generally don't have the benefit of a fourth-wall perspective to this in knowing that their timeline isn't necessarily "prime" by any means.