Here's my idea on how the timelines work:
TOS --> TNG --> DS9 --> VOY
FC --> ENT --> TrekXI
TOS, TNG, DS9 and VOY are all part of the "prime timeline".
FC being First Contact, essentially started out what we now know of as the "alternate timeline". The destruction of the Borg Sphere over the Arctic, Cochrane's knowledge of the Enterprise and the Borg etc. So it really was Picard and the Enterprise-E crew who started us all out on the altered timeline. A timeline which was further distorted by the involvement of Nero and the destruction of the USS Kelvin.
First with the knowledge of advanced cybernetic creatures from the future, and later with the destruction of the USS Kelvin by an alien with advanced futuristic technology, ultimately lead to the leaps in technology, leading to ENT and Trek XI appearing much more advanced compared to TOS.
Haven't really been able to explain how the Enterprise-E was able to return to the prime timeline, but I suppose one could use a "technobabble" explanation, stating that the Enterprise was somehow protected from changes to the timeline, similar to the changes which originally allowed the Enterprise-E to witness the "altered Earth", and also travel back in time.
Conclusion:
TOS, TNG, DS9, VOY, ENT, TrekXI
All of them belong to Star Trek canon, regardless of your general feelings about the new movie or the ENTERPRISE television series. Part of canon, albeit part of an altered timeline.