You have a point. Let me elaborate my thoughts on Flask a bit further.
Personally, my experience is that for rapid prototyping, there's nothing better than starting with the absolute minimum possible, and with a full-blown monolithic framework, the absolute minimum is, more often than not, too much.
I prefer starting a project with a couple of files, like fabfile.py and app.py, than starting a project with a bunch of directories and tons of blueprinted configuration files. It's hard to explain why, I just feel it's a lot easier for me to evolve an idea, from a small prototype to a finished product, with this approach. I guess the cognitive signal to noise ratio is just higher that way. I know many people share this feeling, otherwise Sinatra and all these Python microframeworks wouldn't be getting so much attention.
I think a good framework is like a good government, consistent, helpful, but with self-limiting interference. I think documentation is way more important than features. I'll take a well written web development patterns guide over a framework that does it all for me under the hood any day. The thing is that Flask tries to be both. Flask's documentation is absolutely fantastic. It is no surprise, of course, since it comes from the same guys who made the Sphinx documentation builder.
I like conventions. I just don't think they ought to be mandatory. I see Flask as a genome of web applications, with pre-defined solutions and information on how to accomplish a series of things, but my application itself doesn't have to be a grown organism from the beginning, it can start small, like an embryo, and slowly grow in size. Flask gives you enough flexibility to employ conventions but also do things differently, to invent your own way, when you feel that you need to.