I think the most important reasons for the problems in the anime industry have already been touched in previous posts. My impression is that too small an portion of the income of a production flows back to the production companies. When the economy makes a turn for the worse they get hit hardest.
DVD sales are unfortunatly one of the major sources to recoup the cost of anime production and that medium is slowly going the way of the Dodo. It's not unlikely that fans still spend the same amounts of money on their hobby but probably have switched to buying other items like mangas and merchandise then DVDs. Given the high DVD prices in Japan that might have had an even bigger impact there.
I think a similar thing is happening in the west. Major retail chains offer less anime (like Best Buy) but Diamond distribution for example has offered more and more manga related content in recent years.
The canned dogs website has an interesting article about the way the cash flows are devided in a typical anime production:
anime bussiness