WARNING: NYTimes is a subscription site.
This is a great article about "floaters". I agree that the higher click throughs are just attempts to close the danged thing.
Of course you can turn off all Flash, or you can selectively block using something like "Adblock" in Firefox. I haven't seen one of these annoying things for a long time, but I agree that when I have seen them they were very, very annoying. They certainly do not give me a warm fuzzy about the sponsor.