I's speculate that Boeing presented the low risk route--nobody doubts they can meet the requirement if they get paid enough. I'd imagine that SpaceX presented the lost cost bid, probably viewing their bid as more of a subsidy for work and risks they are undertaking regardless.
EDIT: Listening to the follow up questions on NASA HQ UStream Feed the following questions and answers were asked (both questions and answers are paraphrased by me, I can't type as quickly as they can speak):
Q: Why did Boeing receive more than SpaceX?
A: Both companies proposed costs for their proposals to acquire capabilities to fulfill the RFP, and the government accepted both.
Q: Why two rewards instead of one?
A: It was in the government's best interest.
"Technically, if somebody were to stow aboard the cargo version of Dragon, they'd actually be fine. I mean, hopefully." -Elon Musk
Boeing's advantage in years of experience extracting the most possible money from the government?
Off topic: it's "making do", not "making due". Non American English speakers pronounce the two quite differently, so this is a really startling error for us...
If they both do not succeed and we assume that SpaceX reached too far, then NASA still looks like the good guy because they gave them a shot.
What's the big picture?
Edit: Comment 8326972 by terravion also suggests picking a single winner wasn't an option, which I wasn't aware of, aside from the issue of the relative award magnitudes.
http://www.spacenews.com/article/civil-space/41891nasa-selec...