I've done both, but I autopilot more. Back when I first got WC3, sometimes I would fly just to fly. And depending on the tactical situation, I would sometimes cruise in Privateer also.
It depends on the game. In Prophecy you must autopilot or you´ll take a long time to travel. In WC1 you can just fly to your navpoints, it takes little time.
Seeing as NOT autopiloting would be one helluva waiste of time, I *ALWAYS* autopilot (unless of course I was in those sticky WC1 situations where I was getting pounded and I just needed to get out of there)
The only time I don't autopilot is when I've taken some damage or hits to my sheilds and I let them repair/recharge before autopiloting. For some reason they don't repair/recharge for the proper length of time while autopiloting.
For WC3/4/P you kind of have to autopilot - otherwise it takes too long, even if you use the afterburner autoslide trick. The only time when I found myself flying manual in WCP was on that mission where you have to rescue another wing mid mission. I didn't know how to select the navpoint on the map so I flew manually. Fortunately I've since found out how to select the navpoint so now I just autopilot.
In didn't use Autopilot only in WC1/WC2, where you actually got to the next nav point before you got bored. It was even usefull not to autopilot when flying the Broadsword to regenerate it's shields.
I think somewhere in the Terran Confederation Handbook 2654 (read: WC Movieverse guide) there's a mentioning about altering the ion propulsion system for increased thrust and limited manueverability... something like in autopilot.
But I like it better the way in Starlancer... just 'jump' to the intended nav point instead of flying there all the way. Too bad, I don't know about the exacts physics of this 'jumps'.