There are many possibilities here, and there's no definitive answer, travel pricing is complex enough just looking at flights when you start talking bundles it gets worse.
First off, this isn't impossible but it's also not always the case, depends on where you're going, for how long and what time of year (also what particular days, weekend/weekday). So I'd just accept it, be pleased and move on.
You'd have to check the conditions on your confirmation to see if you need to stay at the hotel, but the most you'd likely have to do is check-in / check-out nobody will check you're actually staying in the room.
So why the low price? First you're booking something on short-notice, generally that means higher prices. Perhaps Expedia have a deal with the airlines where they pre-buy X seats on a given route at a much lower price a long time ago. Expedia knows from experience that they can sell enough to cover the costs, the airline knows that they have some guaranteed money which is good on flights that might not otherwise sell out. The same goes for hotels.
I'm assuming the flight you're getting is the same as one of the ones you priced separately -- i.e. Expedia hasn't given you a charter flight or linked two different ends together.
It may just be that Expedia gets a discount from some airline that's not available to people booking directly.
As I said, there are lots of possible reasons, if you let us know where you were going (and where from) it might be possible to come up with something more specific.