I think it depends on the rate of acceleration. Although the G in an aircraft can change rapidly, a rollercoaster's G may change even more quickly because you are being snatched around a very tight track. If your stomach, and all other organs come to think of it, are suspended under 1g and then suddenly are free to move where they want, you are bound to get a strange sensation. If this happens more gradually then the sensation may not be as pronounced.
Another possibility may be that on the rollercoaster you are being pushed through to some negative g, and 0g is only felt for a split second. It would be the negative g that would make you feel strange, I would have thought. I've only done a few aerobatic flights, but I always thought the negative g was comparable to jumping of a diving board - the sensation of falling and the instinctive panic and adrenalin rush associated with it.
Or it may just be that you're a tough, hard-ass fighter jock who isn't bothered by little things like longitudinal acceleration
.
Kind Regards. Ginge
[Didn't realise most of this had been said above.
Apologies]