I am one of those people. There was a bonus for every patent granted. They were telling us that we need to big patent arsenal to fend off against IBM. It turned out that Splunk is IBM now.
I am against software patents and choose to ignore all pleadings from my employers regarding patent filings. IMO, the bonuses (~$1-2K) are not worth going against my views.
Your last sentence is rather dismissive and seems unnecessary to make your point. You're assuming that they share your views on software patents. They might not. Or at that time not realise the issue with software patents in the first place.