The small high-tech company I worked for was—as discussed in the article—on the other side of this issue. Patent trolls claiming to have patents on basic concepts in computer programming pounced at IPO time (when small companies are most vulnerable to this sort of thing). E.g., one of these trolls claimed they had a patent on the idea of using "sliders" in user interfaces.
Doesn’t White Castle hold all patent rights on sliders?
The truth is, it can take 4 years to get a patent but a large company can kill you in a nanosecond with competition. Even if you do get a patent it can take millions to defend in court against a larger company with more dollars.
Patents are just a license to hire a lawyer.
Can’t afford a lawyer? - don’t get a patent.
There is a massive difference between trade secrets and patents. It is extremely difficult to protect either anymore except through strict secrecy and that isn’t always possible.