AS long as you know the basics of orbital mechanics, flying rockets manually quickly becomes boring. Tedious even. To me (and many others I'm sure) the fun is in designing the rockets/stations/bases and building up a big space program. MechJeb allows me to fly the rockets in a consistent way so I can focus on making them more efficient, and adding new tech as it becomes available. I'm sure you can build a huge space station by flying manually (and I'm sure someone have), but I'm not going to risk destroying it on the umpteenth docking attempt by fumbling on the keyboard.
The Apollo flight computers did most if not all of what MechJeb does; the lander even had an auto-land computer, so I'm not going to lose any sleep over "cheating"...