Much of Once Upon a Time's pilot is spent setting up everything, because it's actually pretty complicated despite the friendly nature of fairy tales. Even at end of the episode there are tons of questions left at the end of the episode, but we get a decent idea what happened. What the pilot doesn't answer, however, is how the show will proceed in later episodes.
The setup in a nutshell: Familiar fairy tale characters, like Snow White and Prince Charming, get their memories wiped by the Evil Queen and are sent to present-day Storybrooke. The mayor the town is the Evil Queen, who also had her memory wiped unless there's a twist later on. The mayor's adopted son, Henry, is biological son of Emma, the daughter of Snow White and Prince Charming who is supposed to save everyone. Henry tracks Emma down in Boston, and Emma brings Henry back to Storybrooke where she decides to stay.
With the rest of the fairy tale characters sans memories, there are lots of pieces the writers can work with. But the pilot doesn't offer much in terms of a story. Things happen, but it's all introduction, showing viewers the fairy tale characters and modern counterparts. We don't get any idea how the fairy tale affects the modern world or how Emma is supposed to save everyone. Given that the show is written by Lost writers, clear answers may be hard to come by.