- You can still have an autopilot for long straight flights. Actual steering is only necessary when you're navigating that asteroid field or zipping through the city.
- The interfaces in the cockpit aren't nice and pretty. There's no neat casing covering everything -- it's a mess of tubes and wires and improvised controls. Buttons don't match, levers don't match, etc
- Nobody can steal your ship.
That last one is a bit misleading -- it's very difficult to steal a ship from its pilot anyway, because they're keyed to the minds of their pilots, and you'd be hard-pressed to forge a mind. When a ship changes pilots, the first pilot has to authorize the next one.
If the first pilot dies, there are some emergency protocols that can be used to reset the ship's computer, but even these are protected by passwords that the pilot will presumably only share with those he trusts.
Short of that option, you can rip out the memory of the computer altogether and put in a blank one, but that takes some serious time and effort -- the computer isn't just one chunk of circuits in one place -- it's throughout the ship.
But with the manually-controlled ship, nobody can steal it because a) it's not set up to receive pilots' implant transmissions, and b) nobody knows how to fly a ship manually. It's just not done.
Except in the case of our hero.
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