I'd quilt them pretty tightly so they have some rigidity. Nobody likes a floppy coaster.
Placing waterproof material inside the coaster may be an exercise in futility. Natural fabrics wick moisture, so even if you had a waterproof layer, moisture would spread through the entire coaster if it's a natural fiber. Another option is to make the coasters out of an impermeable material like vinyl, but then any stitches would puncture the material and compromise its waterproof quality - and, you've already chosen the fabric, so this is a moot point.
The biggest risk with glasses on moisture-sensitive surfaces is condensation running down the outside of the glass. A fabric coaster would absorb that minimal amount of moisture without becoming waterlogged and would protect the wood with its "blotting" qualities. If a drink is knocked over, it doesn't matter how the coaster is constructed.
Last edited by Manalto; 10-31-2015 at 08:35 AM.