It is several things:
[1] Yes, the thread count and the quality of the material used.
[2] The quality and depth of the dyes used. Cheaper fabric doesn't have the same quality dye.
[3] The number of finishing steps used in making the printed fabric.
Some fabric companies do fabric for different stores. The cheaper and least costly for the WalMart type stores; then that for Joann's; then they sell the end of roll to some quilt stores at a discount because it is literally the end of that fabric line; then the best is for our LQS's. You absolutely do get what you pay for.
However, if you want something that will be abused and it is OK for it to wear out relatively soon, then go with the cheaper fabric. If you want an heirloom quilt to be loved and kept, then go to the LQS.
ali