Most food scientists say that salt is ok, that it doesn't inhibit softening and is needed in the cooking water to properly season the beans.
My experience backs this up 100%.
But they also point to acid ingredients, hard water and old beans as the primary reasons why beans fail to soften when cooked.
I have had trouble with recipes that call for a significant amounts of acid (tomato, wine, vinegar) added up-front to the cooking liquid.