Star Trek has been time traveling since the Naked Time. By some current theories and the one used in JJ Trek, if one travels back in time and alters it, a new branch of the time line is created. So wouldn't the Prime time line had ended in the Naked Time episode? And branched again each time they went to the 60's? An I guess earth was destroyed by the Whale probe in the time line they left when they went to the 80's.
I HATE TIME TRAVEL.
I suppose it would depend on your point of view. Some people can argue that, as you said, every little instance of time-travel/meddling/whatever in the Trek universe created a new universe, and there really is no "prime" universe per se.
However, I believe the most popular line of thinking is that even though there are several of these changes that happened, if the changes really didn't do much of anything, then it's still considered the "prime" timeline (or the similar thinking that those changes were "always" meant to happen, so the prime universe was not in fact changed at all, but is continuing the way it should be despite the timeline changes).
IMHO, ENT, TOS, TNG, DS9, VOY, and all the films (with the exception of the Abrams movies) all take place in the original "prime" universe, simply because that was the intention of each series' or movies' creators, and there's no reason to doubt that, even though there are huge tech differences between a prequel filmed in 2000 for a show filmed in 1966.