The prices for B&Bs are higher because they have less rooms. For example, 6 rooms versus a 200 room chain hotel so naturally the operating costs for staff, maintenance, advertising, etc... will be higher per room. B&Bs are about the charm, the character of the place you are staying.
It is a great way to get personalized service instead of being treated like another overnight guest at a chain hotel but in the end, it all boils down to how much time you plan to spend in the room. If all you need is a place to sleep and shower, you could use the YMCA (not recommended) but if let's say you are on a long road trip, 2 or 3 weeks, and want to stop in a quaint town like Savannah or Charleston for a few days (two or three) and leave with a memory, it is well worth it the experience of relaxing.
Also, a common practice I use for booking B&Bs is to ask for last-minute discounts, I have saved up to 40 percent off the listing price if you just rolled in to town and they still have an open room that is not booked. They rather get something than nothing. Fridays and Saturdays are always more expensive than Sun to Thurs.
Where were you thinking of booking one at? What town/state?
