I contacted a colleague in the route charges office to try to get the answer to the question about route charges for humanitarian flights.
The bottom line is these flights ARE billed for en-route charges.
It seems, however, that a waiver of such charges can be negotiated with individual states (it appears from earlier posts that this has already happened with NATS in the UK).
Apparently the problem with an automatic waiver of charges is identifying the genuine cases. It's a sad fact that the unscrupulous put in whatever status will give them the desired result. STS/HOSP was used regularly by some operators to avoid slot delays a few summers ago when there was no legitimate justification.
I would imagine it would be easy enough to identify the genuine cases in this instance though, and I cannot believe that any such request would be turned down. I'm not sure how the mechanics of such a request would work, it would be easiest for the operator to make the request, but more credible if the request were to come from the organisations doing the chartering. Somebody needs to point them in the right direction though.
Perhaps a list of appropriate phone numbers or addresses posted here for redistribution by Ppruners to the charities involved would start the ball rolling........