Personally, I don't see it. I love Star Trek, and I loved this movie. For one thing, the writers took great pains to stay true to established continuity. For another, they took the time to write an explanation for any weirdness with the continuity.
The new movie is different from previous Trek films and the various series. It's more action oriented. The characters have to be re-introduced to newcomers, and to a certain extent, long time fans as well because of the re-boot. Obviously, re-booting everything in an alternate timeline will upset someone, but so far I haven't seen it.
I think it's pretty obvious why Abrams directed the new movie. While Abrams has been successful in TV, he's only directed one other movie (Mission Impossible III) If Abrams wants to be movie director, directing a major studio picture is the way to go.