Grab a successful project already done by someone else, put it in your repository, back it up, and start changing things, one at a time. You'll start to see how little things work, maybe understand why the original author made choices, and surprisingly, find better or more interesting ways to do the same thing. (I'm always looking for ways to do the same thing with "less". I usually find them.)
Keep restoring the original and repeat. Then start adding new functionality. Experiment. Break it. Play "what if". You can always restore and start over.
Before you know it, the mystery starts to fade and for some people, the fear does too.