The whole alternate timeline thing is the explanation preferred by modern scientists for time travel (well, to discuss it in full would go wildly off topic) but basically it's thought the universe avoids paradoxes by splitting off timelines. The idea is if you go and say, assassinate your grandfather in the past, it becomes its own separate reality where things can happen differently so no blowback affects the timeline you started from.
Hence Nero's shenanigans during the film make it an alternate reality, and thus the canon of the previous universe is preserved, no destruction occuring.
Exactly. And although I don't think this is going to happen for a very long time if at all, they could still set future movies and TV series in the original Roddenberry/Berman timeline.