I thought it was simply some kind of "gravitational" answer (and in some cases it is - if you travel very close to a planet you'll go quite "slowly" even at max throttle, but get out of the gravity well and you'll speed up rapidly).
But generally - it's just to make the re-entry procedure easier for pilots, without making it all automatic. If you're looking for an in-universe explanation - assume any FrameShift Drive (which always sounds like "Friendship Drive" to me.. awww!) has a built-in safety device / pilot aid. Without the automatic deceleration, there would be some problems:
- Letting the player do the braking themselves, which would lead to ridiculous overshoots. Travelling at 1000+ times the speed of light (that's ~300,000 km per second) and trying to get your ship to within 1,000 Km though stabbing the brakes at the right time? Not going to happen. You'd have a window of ~ 0.00333 seconds at that speed. I'm 41, maybe my reaction times are a bit too slow for that now.....
- Giving the ships Insane Braking Ability(tm). The ships could go from 1000+ c to 0 in the space of 1,000 Km (by my calculations, that's about 4,582,484,726 negative G; but that could be very wrong). That would give you quite the headache, if anyone ever found your head or what's left of it.
They could just make it all happen automatically, but I actually prefer the challenge of it and getting it done right and quickly. I even developed a different method now than when I started: now I go full throttle all the way, until I get the Slow Down warning (too late already). I zero the throttle until I'm fight underneath the planet, then (with the throttle in the blue zone) I loop back around and inevitably I end up 1-5 Ls away from the planet and travelling at the right speed to cruise the rest of the way in quickly enough. It's less fiddly, and feels a lot faster.