There's no canonical answer to this that I'm aware of.
Speculatively however the answer could lie in the fact that by traveling on the Delta Flyer the Doctor was operating far outside of the environmental parameters that Dr Zimmerman ever anticipated. Since Transwarp velocities were not available (or anticipated to be available) when the Doctor's program was being developed there would be no reason for his matrix to be written with them in mind.
His program can clearly perceive the environment around him in a very human-like way in order for him to do his job and this would almost certainly have to include ways to perceive balance and motion, starships move rather a lot after all, and it makes sense for what is essentially a simulation of a human to communicate those "sensations" in human terms. So "My program is experiencing g-forces and other physical readings outside of expected parameters" translates in human terms to "motion sickness" - which is, if you think about it exactly what "real" motion sickness is.