It's fun and it adds depth! Bunnyhopping is easy to learn but hard to master, and (together with related movement mechanics) adds a lot of freedom and dynamism to the game.

Of course, simply adding bunnyhopping to a game built around more realistic movement will drastically change how it plays -- probably for the worse, if the original was well designed. But in the case of Quake it turned out to open up the game in a way that is both superficially fun and competitively interesting. Nowadays the games in the Quake lineage are built around the existence of bunnyhopping and/or strafejumping, and their maps are designed accordingly.