software <-> company

At artima I read that Paul Graham thinks:

There is a contradiction in the very phrase "software company." The two words are pulling in opposite directions. Any good programmer in a large organization is going to be at odds with it, because organizations are designed to prevent what programmers strive for...

I think software just works different than a company and that's what people running a company should come to understand. A "software company" should be driven by software, not the the company!