I love it when I get a 'bargain' at a thrift store, and I don't think I am cheating any non-profit out of anything; the price they mark it at is actually what it's 'worth' on that day, to me. And if they price their goods too high, they don't sell, and thus don't help anyone. However, I also agree with you; in an action environment like shopgoodwill.com, the buyers set the market price, and whatever it goes for is also what it's 'worth' on that day to that buyer.
It helps them to expand their pool of potential buyers. How many people within ten miles of where I live actually want a pair of 40 year old speakers besides me? But expand that market by putting it online, and prices can go higher for some items.
I enjoy buying at thrifts and saving money - and helping others. It works for me on both counts. I don't begrudge them the money they make putting things online to sell; if it's more than I want to pay, I don't bid.
And the important thing to me is that Goodwill actually *is* a legitimate non-profit, helping the community, and I commend them for doing so. I'm glad they do what they do, along with the others I know of in my area, like Salvation Army, St Vincent de Paul, and Grace Centers of Hope.