Good development practices and project structure, generally good code examples, fewer bugs and tested code and re-using code are all very important things in any development, and frameworks all help with that.
If you are starting some of your very first web development, I'd encourage you to play around with some low level Node.js HTTP stuff, or even write a web server in another language, to get a feel for how the request/response model, HTTP header/body sections, etc, all work.
But after that basic introduction, dive into a framework and learn it well. The projects I know that were developed 'without a framework' are more often than not poorly structured, poorly documented, and difficult for new developers to learn their way around, precisely for the reasons given at the end of the article.
If you evaluate frameworks for your use-case, and realise there isn't one that suits you well, then by all means, go and make your own, but don't just make your application - make a framework for your application, and then use the framework, it will result it much better structure and better software engineering practice.