It's funny how people think that but the only time they were ever dead was the flash sideways in season 6, hell they even had Jacks father basically say the whole other season were real life but that sideways flash was the afterlife, they couldn't make that any more obvious.
Jack was always the main character and in the end I liked how his life played out, everyone else along the way had an awesome story to tell as well. They could of shot off in so many directions but I liked how they finished it.
Also the end credits with the smashed up plane, I know that confused a ton of people. I think it was actually ABC who put those scenes in on the credits so it wasn't just cut to black with the normal credits. I didn't like the crash credits at the end.