It's fine to use cotton-poly fabrics for quilting. There are just a few things you need to take into consideration.
Poly-cotton does not fade the same way cotton fades; it retains its original color. This matters if you are making a quilt intended to last a couple of generations, as the fabrics will not fade together. For example, look at the soft colors of a 30s quilt that has been used. Poly-cottons would stand out in a vintage quilt.
Poly-cotton frays more easily than cotton. As long as you are aware of this and can handle it, no problem.
Poly-cotton does not crease as well as cotton. This can become problematic with applique, where you want sharp creases while sewing.
Poly-cotton is more slippery than all-cotton, making it a little trickier to achieve accurate seams. This is more of a problem for beginning quilters than for people experienced in piecing.
Edit: To answer the original question, I think it became customary to specify 100% cottons for quilting simply because it avoids all of the above potential issues.