If there's any truth at all to negative test screenings, it may not have as much to do with the story that was told as the type of story that's told. It could be audiences were hoping for a space adventure, especially for the fiftieth anniversary, the "boldly going," and all. Instead we seem to be getting (at least mostly) a planet movie, and the test audience was disappointed. It could be the audience was soured by the early exit of the Enterprise and never recovered. That said, the odd thing is, one of the most popular Trek movies, TVH, didn't feature the Enterprise at all in any meaningful way. There was just the cameo at the end. Maybe the movie wasn't "Star Trekky" enough, either. Could Orci get the last laugh on that?
One thing's for sure, since they are redoing the ending, let's hope it goes in TWOK direction and not GEN.