In  Bilski and software patents, Rob Tiller (vice president and assistant general counsel for Red Hat) attempts to make a case against software patents by claiming that they are abstract and therefore not patentable:

In view of this serious problem, Red Hat submits that the Interim Guidance should be revised to recognize that software patents will ordinarily fail to satisfy the requirements of 35 U.S.C. Section 101 as interpreted in Bilski and prior Supreme Court cases. Software is essentially nothing more than a set of mathematical algorithms expressed in a particular programming or machine language. As the Bilski Court recognized, mathematical algorithms, by themselves, are abstract ideas that are not patentable.

The problem with software patents goes far beyond being an abstract mathematical algorithm or not, since most software is  about ways of doing business or implementing consumer electronics,  as opposed to innovative computational algorithms.
If you have any doubts regarding the willingness of the USPTO to issue software patents as ways of doing business I suggest taking a look at a  System for calculating a support payment in a network-based child support framework, a software patent issued Oct 13, 2010 for tracking parental financial support. Not a set of mathematical algorithms at all and not expressed in a particular programming or machine language.
The problem with software patents is lack of notice and boundaries.
A real estate property has clear physical boundaries.   A small molecule has clear chemical boundaries.  Software has practically no boundaries at all since you can implement the product in Ruby or PHP or C# or Erlang if you like.   Since the PTO does not require a proven, working implementation  – the boundaries are ephemeral.
Not having boundaries leads to the problem of notice.  Inventor A invents some software for an innovative social network and Inventor B invents some software for network analysis.   It is almost impossible – considering the abstractness of the two ideas and the volume of software patent applications  – for the inventors to be aware of the prior art.   If you are doing B2C commerce online – you are probably infringing on over 2,000 different patents.
If you did get a software patent – then the notice problem may boomerang on you years later – as another inventor discovers your work and sues you.  Consider NTP versus RIM
An attempt to rule out software patents by Red Hat, claiming that they are abstract mathematical algorithms is what I would call a nice try that doesn’t hold water.
Unfortunately – I do not have a better solution, but it seems to me that it would be a stronger intellectual argument to claim that until software notice is resolved – software patent applications should be reined in.