If you don't have a spare bedroom to use it in, then store it high up in the linen closet or in the attic. If the giver asks about it, say you tried it and find a box cover cumbersome to use. (This really only works if you don't use other tissue box covers.) And then hug her and assure her that you still cherish the thought. Don't even say you cherish her efforts, because you don't want to be rewarded with more of them.
If she asks or says you didn't like it, be frank. You don't like cross stitch or whatever the reason is. If she gets offended, hey, it was a tissue box cover, nothing major.