I think you're right to be concerned, but I don't think it's as bad as you
think it is. There are a LOT of on-line story sites and they're all doing well, as are sales of e-books.
As an author who does a lot of writing and supplies the end result as a print ready pdf for a printed book or sale as a pdf file, and often also provides a version to be read in html, I AM very worried about the way the e-book industry is going with a lot of the books they provide for reading via iPad, Kindle, Nook, and tablets. The issue I see there is a variety of mixed formats and NONE of them retain any reasonable presentation format to make them look even remotely like a book or something that can easily read on-line. It's because of this I create pdf files for e-books only, despite one of my publishers allowing another publisher create some books as mobi and nook files.
The fact my books are available on-line and thousands of copies have been downloaded and read, and all up we are talking of thousands of millions of copies by the time you add in all the authors whose books are available on-line, means that reading comprehension can still be retained, but being able to read a sensibly laid out book on-line is damned hard due to the format fight between nook / kindle / iPad / etc all providing horrid presentations.
Edit to add - there is also a difference between being able to retain reading comprehension and those not interested in doing so at all - think of those who love leet and txtng.
