I guess the two sides of the coin are described well. One side is the cost per logbook hour, which is what the pilot feels, what she/he is interested in and what can be measured quite easily. The other side, the real TCO cost per flight hour is seldom really gathered beforehand, so discussion is always off balance on facts basis. Usually a company doing charter tries to guesstimate total costs and expected flight hours, but this is seldom done well and falls under risk of commercial operation (and as such, the uncertainty has to be paid for by itself).
Charging per Hobbs, per OffBlock/OnBlock or per Airtime is doing nothing to the total costs at the operator, it only shifts distribution throughout the users (or should do). If you complain on the way you are charged, you are trying to get money out of the pocket of another fellow pilot, please keep that in mind. Looking at the very bad commercial numbers of the usual charter businesses, I suspect that many didn't recognize this and pulled money from the survivability of the businesses.