I'd tend to agree that things aren't so hopeless in the longer term. Let's see where this case leads. Certainly Oracle and the smartphone bun fight are also beginning to focus a few minds. I think if you grouped Linux users, including android people, they would be able to wield some serious political clout. The conditions imposed on the purchase of Novell's patents were a clear sign.
That said and speaking as a *complete* non-expert, I'd really expect this decision to be overturned, if only for the screaming defence of the code not having changed since before the patent. But also it seems that inventions that aren't linked to specific machines (rather than a general purpose computer) may be in trouble after Bilski.