Couple of things to keep in mind. They do have their fabric line and threads manufactured for them, to they do not have to go through a warehouse/distributor to order those - one less markup. They probably also buy their books directly from the publisher - one less mark up. Quilt Shops are ordering Fabrics/Books/Notions, etc. from a Distributor therefore they are paying an additional markup that in itself is a HUGE difference.
An internet only shop does not have to pay for: Rent, utilities, liability insurance, employees, etc.
While you may (or may not) get a better price on items from internet only shops - you also do not get any of their expertise: Help with a pattern/fabric choices, nor can you go in an look around when you just need to get out of the house or have some adult company who understands your hobbies and can put you in a much better mood