Why was it decided to ship javascript programs in plain text? Was it to achieve performance enhancement or the authors never imagined that javascript will be used in much more complex applications and developers may want to protect the source code?
That's because JavaScript was never intended for large web applications, rather it was a way to do something "cool" on the browser. JavaScript wasn't a very popular language and was despised until the advent of AJAX, that is why there has never been much insight how JavaScript should be distributed. After all, simplest way to send JavaScript to a browser was through regular text files, why would they have bothered with anything else back in 1995?