I made the recipe as stated. After the 3 hours in the oven, the beans were still not cooked. It did amaze me that the recipe did not state to pre-cook the beans. I think that should be done. It also does not say to soak the beans. It is best to soak the beans overnight to disable the enzyme inhibitors present in most beans. I did enjoy the flavour of the fondue.
Instead of soaking, I would suggest rinsing the beans briefly, to remove any dirt that may be on them, and then pouring BOILING WATER on top of them, until the water is two or so inches above the beans. Soaking dry beans leeches away minerals that give beans their flavor. Adding boiling water to dry beans locks in their flavor -- a bit like searing a piece of meat. Simmer (not boil) the beans uncovered over medium heat until their skins are soft (about an hour and a half), adding more HOT water as the cooking water evaporates. Salting the beans or adding the fondue before the skins are soft will make the skins tough.
It should be noted, Lisa, that step one instructs the cook to soak _and_ cook the beans. I'm sorry that your cooking didn't work out as planned. It is amazing that 3 hours of cooking didnt' kook the beans, tho!