Welllllll....
I'm not sure why she can just rifle through your stuff. That would bother me. So, yes. Stand up for yourself.
Can you head her off at the pass? Like, where's your stash located? Is it in a "common area" of the house? Is your sewing room an actual ROOM that can be closed off?
In the future, if she announces she's going to shop your stash, engage her by asking what she's going to make. Ask if she's started choosing her fabrics yet. Somehow, turn the conversation to HER going shopping at a REAL store so she can select what she wants, and if she gets stuck or needs something to give it va-va-voom, bring what she's chosen over and you'll help her find something to complement what she's already PURCHASED.
If she's a little off, she may get bent outta shape anyway. And since DIL knows what kind of person SHE is and what kind of person YOU are, you're in the clear.
It's not really a matter of if you paid $1 a yard or $10...YOU selected YOUR fabric for YOUR stash. If she wants to start quilting, GREAT. But it's a very personal thing to select things for yourself, and she should take care in shopping, and not just TAKING from you. It's good to share and cooperate, it's not good to take advantage. She may not know that's what she's doing, but she sure sounds like she feels entitled.