Historically, federal circuit precedent said exactly the opposite - that when a generic computer was programmed for a specific purpose, it was now a special purpose machine and patentable.
1) Your argument does not refute the GP's statement. A "specific purpose" is not necessarily an "abstract idea", depending on how the claims are structured. A claim saying "presenting ads in such a way that it is unobtrusive on a computer" is an abstract idea[1]. A claim that specifies how a computer can, say, examine visual or DOM elements on a page to determine where to place ads such as not to be obtrusive, is much more concrete.
2) A generic computer running a program is a special purpose machine: it's now doing things it could not do before it was programmed to do so, and as such, it is performing potentially novel functionality. Otherwise, in my mind, you might as well argue "a kitchen knife could not be a murder weapon because it's a kitchen knife."
> This decision should, if the federal circuit actually follows it, knock out a large set of software patents.
I've looked only at a few particular areas, but all the "old idea, only on a computer / on the Internet" patents I've seen so far (like [1]) the one should have expired by now. However this is purely anecdotal, of course.
1. Such a claim (I only paraphrased it a bit) exists, and was referenced in one of Lemley's papers. On mobile so can't find it right away.