I was originally a bit let down by the obligatory Hollywood happy ending, preferring the threatened Twilight Zone-esque scenario in which he gets mind-wiped, thus being doomed to go on missions indefinitely, particularly as the ending we
did get seemed to totally go against the story's own logic. But, while I still think a darker ending would've been more effective - fan editing opportunity alert! -
this message board post does go a long way toward making it make sense:
''I liked that Rutledge's bullshit makes no sense in or outside of the movie because he was clearly lying to Coulter to keep him from realizing the truth: Rutledge was sacrificing the lives of people in other realities, who could be saved, to further his own ambitions for the project and to save "his" America's citizens. If Coulter realized he was letting real people die with all of his failed attempts, he might have been unable to continue or focused more on saving each train load rather than looking for the bomber. Hell, he could have lied to them once he figured out how to beat the scenario and save the day in the AUs and gone in again and again, pushing it right up until the last second necessary to also save his own reality's Chicago from the dirty bomb.''