I think there really is a difference in quilt shop fabric vs. chain store fabric. Technically speaking, quilt shop quality fabric has a higher thread count which produces a silkier finish, less bearding when quilted, and a longer fabric life. In my longarm quilting business, I can usually feel the difference in fabrics.
That being said, I don't think it's wrong to use chain store fabric. You need to take into account your personal fabric budget and the purpose for the quilt (is it a play quilt or a wedding gift family heirloom?) With the price of fabric these days, many of us have to consider these questions. I like to take advantage of local quilt shop sales and build my stash at those times, especially backing fabric.
Ultimately, most of us make quilts out of love, with the fabric coming in second place. :)