Ok so it's totally possible that I am being an incredibly slow fan but I've only just realised the connection between the quote in the title question and Dean's other quote "So what are you gonna do? Just live some normal, apple pie life?".
But when Dean is tied to the tree in Scarecrow and shouts "I hope your apple pie is freakin worth it!" he may not only be shouting at the people who put him there to keep their apples growing well, but he could also be talking about Sam leaving him in search for a 'normal' life and putting him in this impossible situation.

mm well. he said he was proud of Sam for leaving before that scene. so I really don't think he was, but technically he COULD be. so good find hun :)

Oh I don't mean he's pissed off with Sam for leaving exactly but that he's in a life threatening situation and Sam has left him. I'm not really explaining myself properly :S

If I was about to get skewered by people who worshiped a sacrificial pagan god, to save a town and its apples... it better be worth it, so I am taking this sentence literally.

At first i put no, but after em-em's explination, you're totally right. I'm having a hard time typing today.

well spotted, a little too far-fetched i think though :) great quote mind ;)

Wow! I don't know that the writers meant it that way, but in the context of the characters, I can totally see him thinking that way! THX!!!

In that episode, Sam had left to try to track down John and get closer to getting his revenge, not to seek a normal life. So I don't think the quote was a reference to that. Dean does tend to use "apple pie life" as a name for a normal life, though.