I think the author is talking about business method software patents. If the business method implementation needs patentable technology to implement, then it may not be such a bad idea.

But again I feel that for an early stage company, filing a patent just helps mitigate the risks in the VC's head more than anything else. Forget about enforcing your patent. If you are successful and you have a lot of money and you feel like bullying your competition, we all know how some successful companies go about it.