I have some pretty basic recipes I cook if I'm a bit tired from work, I can make them without really thinking (e.g. diced chicken + green beans & cream + pesto.) Fortunately, the nearest shop is about 2 minutes detour from my route home, so I can wander in and buy the things I'm missing.
I think one way to build up intuition is to cook a recipe with a very short list of ingredients multiple times, with small variations (like the size of cutting things up or cooking time or whatever).
One thing Good Eats consistently does is talk about whether an ingredient has a functional purpose in a recipe, and what that purpose is. Other cooking resources do that too, but usually not as well.
This is obviously a rather trivial example, but hopefully you see how generalizing this (and similar nuggets of information) can help.
I've been trying to learn how to cook ever since I moved roughly 3 months ago. My early attempts at replicating others' recipes had paid off decently so I attempted the hack-stuff-together approach on a couple of occasions. It did _not_ go well. :-/
I ended up with a ton of wasted ingredients not to mention the significant amount to time spent in prepping and later, cleaning up.
That said, I agree that (with a bit of experience) this approach to cooking is a lot more fun. As a comment elsewhere on the page says, cooking for yourself could sometimes be a pain (especially after you get home from work) and thinking of it as a side project really helps.