I was watching TNG the other day for the first time in years and I had to ask myself if there is any need to helm or navigation. Surely the captain/first officer could just tell the computer where they want to go and when they want to arrive by, and the ship can steer itself.
Captain: "Computer, Set course two-one-three Mark seven."
Computer: ""Unable to comply, the automatic pilot system is offline."
Automation is all very well and good, but like any system it can fail. Today a plane could take off, fly to it's destination and land all by itself." But would you fly on it without a pilot?
As for having a dedicated department, sure everyone might receive basic training in piloting a starship, but their is a difference between basic and advanced training.