When I learned to fly airplane, I was charged engine running hours. I thought that was fair - I logged engine running hours.
When I learned to fly helicopter, I was charged engine running hours, less .1 hours per flight. The rationale of the training organization was that they did not want their students rushing through checks, so they would absorb that cost, to encourage good practice, and risk of an unsafe situation from something being missed. I liked that policy.
In the end, if you're paying for more aircraft operating expense than you are logging as the pilot, something is wrong.