Someone around here will know better than me, but Mighty Fine MLP products are licensed by Hasbro. This includes fan made designs. I have never made a design for WLF so I don't know what their contracts are like, but I imagine they have to sign an agreement saying that WLF/Hasbro now own the design and can use it for their own purposes. A lot of the designs originally used for t-shirts are rehashed onto art prints, wallets, bags, and even vinyl toys, and sometimes sold in retail stores like Hot Topic (although I don't see this as often as WLF's "original designs" using vectors and the like).
I doubt Hasbro would have let WLF amass such a collection of MLP merchandise if they weren't getting something out of it!