To say to not using any game engine was maybe exaggerating, but I believe it is important to understand the basic concepts. And when the goal is, to make a flappy bird like game, the canvas and some scripting would be a good start, I believe, if there is zero experience.
On the other hand, I also started with Adobes Flash. You could draw and animate and script right away ... and get awesome results right away .. without having to google html audio element.
There's much to learn in game development on itself, so using a dedicated library that will make the simple tasks easy is always a good idea.