Some confusion is perfectly normal at this stage.
I skipped Source Code when it was in theaters back in April, but now that I've caught up with it on DVD I really wish I hadn't. For one thing, as much I tried to avoid them I've still had a number of key plot points spoiled for me (so I promise to tread very lightly here). For another, I was impressed enough with Duncan Jones's debut, Moon, that I should have had faith in his ability to choose a follow-up. Mostly, though, it's just a cracking good science-fiction thriller (albeit one that plays like a cross between Groundhog Day and 12 Monkeys at times) and should be recognized as such.
It's possible to get the gist of the story from the trailer -- Army captain (and Afghan War veteran) Jake Gyllenhaal is thrust into a situation where he has just eight minutes to discover who planted a bomb on board a double-decker train bound for Chicago, and each time he fails he gets sent back to the beginning to start over from scratch -- but as it develops Ben Ripley's twisty screenplay reveals a multitude of layers, most of them wrapped up in his interactions with the beautiful female passenger seated opposite him (Michelle Monaghan) and the government agent talking him through his mission (Vera Farmiga). Gyllenhaal has less face time with the doctor in charge of the project (Jeffrey Wright), but then again they have different reasons for wanting him to succeed. Whether he does (or not) I'll leave for you to discover if you so choose.