To some degree, I think it is because the offline brands bring baggage with them online. Take Barnes and Noble - great offline brand. But I've walked into a Barnes & Noble store and walked out empty handed because they didn't have the book I wanted in stock. That's not the web experience I want.
The web is limitless, access to all information at my fingertips. So I go to Amazon instead. The only brand memory I have there is that no matter what the book I am looking for, they have it. They are the universe of books. Barnes and Noble might, in reality, be limitless as well, but that's not what their brand perception is to me. It means Barnes and Noble books, not all book.
To some degree I think that type of brand baggage keeps Yahoo as the Avis (#2, but trying harder) of the search industry. Their roots were as a directory. A directory is, by definition, limited. But search is supposed to index everything - and that's what Google stands for - the universe of the web. So I am pre-disposed that when I am searching Yahoo that my search result isn't as complete.
Same goes for news. Producing their own content turned out to be a double edged sword for the newspapers. Yes, they had their own content - which is great - but it also meant that they weren't interested in promoting anyone else's content. So I know when I go there I am not getting the universe of relevant content, but rather a limited set. Even if a newspaper did have the right aggregation technology and content mix, if they brought it online under an offline brand name my guess is that it wouldn't be the winner. The offline would have the baggage that the experience is limited - and consumers wouldn't want that.
Knowing the limitation of your brand is hard, but something to keep in mind as you migrate your business to new mediums.