"after all, how much can you actually save by [skipping a flight]"?

Many airlines have complicated pricing models that attempt to capture market demand.

For example, I just looked up flights from Portland, ME to Los Angeles, departing on Jan 19 and returning Jan 26. If you take US and connect through Philadelphia, the cheapest price is $309. If you were to fly from Philadelphia to Los Angeles non-stop on that same day, it's $399 - 30% more expensive! If US were to allow you to skip the first and last part of the Portland-Los Angeles trip and get on and off at Philadelphia, they would receive substantially less revenue.