Django's a huge, monolithic framework that you need to run a script for that generates some files and a folder strucutre.
Flask is a microframework. You can create a flask app contained entirely in one file, or on spanning several. It requires a minimum of configuration to work.
I'd like that misconception to finally be dispelled. In spite of being installed as an apparently single entity, Django is modular. You can use SQLAlchemy and Jinja2 with Django, and you can use Django's ORM all by itself, or its templating system standalone. You can use Django without manage.py, and while the only actual requirement is settings.py, that is in the process of being done with.
Flask is a microframework. You can create a flask app contained entirely in one file, or on spanning several. It requires a minimum of configuration to work.