For me, that actually worked better. If you start with a fully loaded framework such as Django (even though it is an awesome framework too), I found it difficult to fully understand whats going on in the background. For example, I personally don't like all batteries and prefer to only have the core web functions out of the box. Flask works for me because it just about gives me enough and not much or too less. I don't want to necessarily build my own WSGI layer but I do want control over how I create/save my user details.

Also you don;'t really need to learn Jinja etc. separately. Flask does enough to get you started. For example, I can easily build routing using app.route() decorator in flask which in the back is using Werkjeug. I honestly don't know much about werkjeug itself (yet) but that did not stop me from building a fully functional web app. Of course, if you really want to get in the details, you learn the individual libraries that gives you flexibility to build a real work production app. YMMV