I'm not totally sure but I believe it works like this:

The person who opens the store buys the button (or whatever) for 2.49 but then they come up with a design and sell the 'designed' item for what they think is a fair going rate... This is why you see 2.49 and 5.99, because the 2.49 is for the blank cup or button or whatever.

These stores are mostly owned by individuals who want to sell their artwork/designs. So they are generally for profit by the person who owns the store... albeit not a lot of profit.

I'd love to come up with some nice designs and sell some t-shirts. I think some of those that are there now are wonderful! Maybe one day I will have a brain flood and have something phenomenally creative occur. Then I'll open a store of my own.