No, Star Trek XI is NOT in the Prime Timeline, and never was.
I was VERY poor and it took me a week to see ST: XI, and then I was very busy and I couldn't get on Trek BBS. I have been looking through threads, and I have not seen this brought up, but it caught my attention immediately.
Star Trek XI took place in a parallel reality. From beginning to end, it was NOT the universe that TOS, TNG, DS9, and VOY took place in.
And here is why...
BEFORE the temporal incursion by Nero, the crew of the U.S.S. Kelvin were wearing the Starfleet Delta insignia. This insignia was also worn by all the cadets at Starfleet Academy.
As shown in TOS, and stated in DS9: Trials and Tribbleations, each starship and starbase had their own unique insignia. The delta was this ship insignia of the Starship Enterprise, and because of the many legendary deeds of the Enterprise and her crew, the Enterprise Delta was adopted as the official insignia of the entire Starfleet.
Thus, as it relates to canon, the temporal changes caused by Nero had no effect on the Prime Star Trek universe. Not because the new movie uses a Quantum Theory of Time Travel, as opposed to a Linear Theory, but because it was always an alternate quantum reality to begin with.
If anything, this is the quantum reality that Enterprise existed in, which makes total sense. The newest Trek TV show is a prequel to the newest Trek Movie, and neither have any relation to the Prime Timeline of TOS, TNG, DS9, and VOY.