Flee to where?
Everyone Jessie has ever known, loved or felt close to it in Albuquerque and all of them are gone, whether in reality or simply in effect.
His "true love", Jane Margolis, has died of an overdose - which he feels unbearable guilt for, considering it was him who got her back into drugs. He still has Badger and Skinny Pete, but he's now beyond them. They're still just stoners, but he's seen and done so much more and is struggling to live just that lifestyle now. He had to kill Gale, unwillingly, to save himself and Walt. At the time he feels he was responsible for the poisoning of Andrea Cantillo's little boy. Even Mike, who he was beginning to feel closer to, is now gone.
All in all, he has a mix of emotions. He feels incredibly guilty over all the pain and suffering he has caused. He feels angry at Walt, the man who gave him so much, yet has taken it all away. His parents have abandoned him and he's in a very dark place.
We see him in Season 5 with the money, eventually, but by then another little boy has already been murdered by Todd. Jessie is partly responsible, as he was part of the heist. Nothing he does takes him away from the drugs, the pain or the death. He could flee, but he's just completely broken at this point. He's scared, unhappy, completely lonely (remember the all day raves just to try and stop his mind from thinking).
As Season 5 continues, we see him simply give the money away.
So as to your question, "why doesn't Jesse flee?"
I would respond that he simply has nowhere to go, nowhere he wants to go, no ambition, no hope and everyone he's ever truly cared about is gone. He's just a shell at this point and so fleeing is irrelevant to him.
