Hi
I think you probably answered your own question;
If your game isn't running smooth, trying to takeoff could be nearly impossible. The old saying "frame rate is life" doesn't just apply to shooters. You need a smooth game to be able to catch the plane as it tries to veer off the straight line you intend to takeoff on.
I ran into this problem when I first got FSX. My pc at the time wasn't strong enough to run it well. I couldn't hardly get the Piper Cub off the ground in the take grandpa to the airshow mission.
It was just too choppy to have good control at a time when fast reactions on the rudder was a must.
Maybe try lowering some settings, resolution, etc. and see if you can get rid of the choppiness.
Not sure why having the aids on didn't help keep it straight though.