Bunnyhopping is often used in first-person shooters not just to move faster, but for many people to dodge. Back in the misty times long forgotten people realized that you'd be harder to hit if you just jumped. Thus, while the average player is probably aiming for your center of mass or in a game with location-specific damage, your head in the hopes of getting a headshot you'll leap out of the way and thus avoid damage entirely or simply take it in a less painful place. If one jump is good people assumed a lot of jumping is better and would thus jump around randomly the entire time to avoid being hit.
Realizing this is irritating and highly unrealistic many recent games have thus implemented some form of stamina. Day of Defeat especially tries to be a bit more realistic than many other mods and provides a stamina bar that slowly depletes when you jump or run quickly or such requiring you to rest occasionally. Firearms and the Opera also follow suit while TFC, Natural Selection, and Counter-Strike (where it can often be quite a problem) leave things as they are.