What type of app do you want to make? If it's iOS, you need to learn Object C. For Android, you need Java (not Javascript). Javascript isn't really a language you could make a whole app in. It's client side, which means it doesn't really interact with the server or database or anything.
Python is a good one to learn. I don't really know much python, but it's a good one to do. Check out
www.codacademy.com, they have a great course for python. I don't know much about code.org or Hour of Code. In any case, once you get the fundamentals of how to code, it's easy enough to learn another language. That feeling is normal though, where you sort of get it without really understanding why you have to do that. It goes away as you get more comfortable with it and learn more hah.