Patent ownership does not imply political support
Why do software companies apply for patents?
- They want to build a portfolio of defensive patents, i.e. they're an money-wasting obligation
- They want to impress venture capitalists. (See statements from venture capitalists for some explications of why this is not important.)
Ownership does not imply support for software patents
Some companies own software patent because they acquired them when they purchase another company.
As Lord Justice Jacob wrote in the Aerotel v. Telco (2006, UK) decision:
If your competitors are getting or trying to get the weapons of business method or computer program patents you must too. An arms race in which the weapons are patents has set in.
Businesses feel obliged
I've never been a big fan of the broad swath of business method patents and even less of a fan of the process for creating and litigating patents. That said, it's the world we live in. So, like every other Silicon Valley entrepreneur, I file patents. 
Related pages on ESP Wiki