There's one interesting quote in the article: Musk: I can’t tell you much. We have essentially no patents in SpaceX. Our primary long-term competition is in China—if we published patents, it would be farcical, because the Chinese would just use them as a recipe book. If your process/ideas are sufficiently complex, it reduces competition if you don't file a patent.
But for industries where that's not the case, like rockets (my current) or to pick another example from a previous job, magnetic bearings for sub-sea tubo-machinery installations like natural gas compressors[1], it makes no sense to file a patent. It's much easier to keep it a secret, because it's not like your competitors are going to scuba-dive down to the compressor control cabinet, whip out a JTAG and see how you've implemented your control loop on an FPGA.
Likewise, if you do patent it, it's very difficult to prove an infringement for the same reasons.
So essentially, in industries where it's not the case that your competitors can see what you've done, secrets over patents is the norm, in my experience, and has been for while.
[1] Mag bearings use electromagnetic stators and magnetic collars on the shaft to levitate the shaft inside a bit of spinning equipment. This means it's entirely non-contact, dramatically reducing wear, especially useful on difficult-to-service installations like sub-sea.