I agree with you. I'd never use polyester thread to quilt a top made of 100 percent cotton. Poly thread is stronger than cotton and over time can cut into the threads of your patchwork. Harriet Hargrave explains this in her books and summarizes the point by saying that it's much easier to repair a broken seam than it is to fix a hole in your fabric.
That said, if you don't expect the quilt to last that long, poly is probably okay.