Let's take Cowes as an example; why would a local council want to pay for the design, construction and maintenance of a bridge that only crosses 15 meters of water? Let alone modifying surrounding roads to go with it when they could have a small floating vessel going back and forth? I assume also that the volume of traffic would be a factor in whether a bridge is built or not.
Also don't forget that in areas where chain ferries operate near larger vessels, the bridge would have to be higher and I'd assume curved. Wouldn't that only work if the terrain on either side was of a similar height? I'm not entirely sure on that as I'm not an engineer but that's what I think anyway.
I don't think all chain ferries let go of the chains for vessels to pass, it seems that the chain only comes out of the water a few meters in front of the ferry as it goes along. I've never understood why this is, I would of thought that before the ferry could make headway the chains would have to be out of the water and taught. The only reason I can think of is the weight of the chain as a whole keeps it submerged until the ferry gets closer.
Mike
EDIT: Angus beat me to it