Honestly i think he had severe mental disorder,and was not treated correctly at first i am glad to say i am doing very well now. Being on incorrect medication myself in the past, the effects are horrible,hallucination, thoughts of death ect.. in the beginning Donnie was not taking any meds, then as soon as he started taking them he was hallucinating,being out of touch with reality, thinking irrational,like the world will end if he does not do what his head is telling him, and in the end Donnie was still not ok hence, death, but everyone else was exactly the same, just as they were when it flashed back to his life before he died.He was not ok then either,but everyone else was. In my personal experience i focused a lot on his mental state in the movie . He may have seen this "bunny" figure before, and it stuck in his mind,(after all wouldnt you think he would of known of his sisters boyfriend frank?) getting fixated on him, as well as portals...where other mental illness can fixate on death murder ect.Like when a murderer says there dog told them to go on a killing spree..Its not because of portals and time travel,its because they are mentally not right.Donnie was out of touch with reality. He was getting worse and worse and was not being treated correctly,I think when the plane hit the first time in the beginning he really died,then went back to show you his life before he died, For example Gretchen was never really his girlfriend , maybe a girl he had seen before but they never spoke a word. Therefore it caused Donnie to fantasized about there relationship when it never even existed, we were watching the movie THROUGH Donnies perspective , the way he perceived life, the way he perceived characters, not how they really were in the movie. Then they throw in all that Mumbo jumbo stuff about time travel and everything to confuse viewers and keep them wondering. i do not believe Donnie was a form of "modern Jesus" i think he was on medication that wacked him out,he got to the point that he felt doomed, and helpless,not caring whether he lived or died. Having to struggle through his life. Like he was so unhappy and confused it was his "destiny" to die from the jet engine.To "be at peace" you could say.

The Director doesn't even tell us what the whole movie means...I think you have to take from it what you will. To me the whole movie is about how Donnie is being shown what is going to happen in his future and kind of being asked if he wants his future to continue...He gets to meet Gretchen who he falls in love with. This girl who totally understands him and loves him back but he can see that she will die and it will be the worst pain he's ever felt in his life...instead he choses to die being crushed by the airplane engine and to never know her than to suffer that heartbreak. I also think it's sort of about Donnie's struggle with life, how people in his town are really messed up like freaky child molesters who try to make him think a certain way . He just doesn't fit in. But When frank says that the world will end...he doesn't mean everyone's world he just means Donnie's.

how long an answer do you want? - In fact a lot of article's and books have been read about this same subject. If you watch the DVD together with the comments of the director you get an idea/although the ideas of the director aren't necessarily important.
I take something different from it every time I see it, which is something that I think is an important quality in a good film. 1. theory is that there is a rift in the structure of time and space as Donnie should have died from the plane engine from nowhere, when this doesn't happen the world is unravelling and Donnie suspects this, the only way to make it good is by dying in the end - the world (his world) dies at that end.
The elussions to Frank are also interesting as he is the one who is dating D. sister (when she comes in after her date you hear the hunk of his horn) and the one who kills Gretchen and who Donnie ends up killing....(I seriously could go on and on, so just watch it over and over again, read articles about it, etc)