your comparison is very poor: never heard of a 'microwave' which is encoded
You touch on valid points, however my comment wasn't a comparison but refuting the recommendation to "never trust properitary protocolls / products / ... once you will be alone " (sic). In our lives, we not only use, but actually rely on proprietary products all the time, be it software or otherwise, and while many of them are not strictly essential, for the most part, life is easier and better for them. I've started playing with low level microwave radiation on a project that I'm working on, but I wouldn't go out and look for an instructables.com project on making my own microwave oven from scratch. I value my life too much and would head for a closed, proprietary, known brand make every time!
Focussing back to software, while there is plenty of good open source software, some of which will have longevity from having achieved sufficient popularity and momentum, it can also be a significant business risk to use open source products, the majority of which are maintained by hobbyists who work on them in their spare time, and who may give up the project at any point in time and for any number of reasons. The web is littered with a trail of promising but dead projects for which there are no updates, no bug fixes, and no support. While commercial products are not immune to the same fate, a product backed by a company is more likely to have a good future than an open source project, provided that there is sufficient revenue generated to sustain its workforce and the needs of the company behind the product. To maximise revenue and therefore product survival, such products frequently need to be licensed and closed in some way, with some kind of mechanism to enforce the licensing, and for PHP scripts that means encoding. Even if it's not for us and against our philosophy (or desire to get software on the cheap, which if they're honest is why most people want OSS), we shouldn't knock the commercial stuff.