I think that you misunderstand
it doesn't cost nothing to accept donations from their partner charities.
they still need to run servers, employ staff and still get charged processing fees by the banks for the funds that they collect.
but for the bigger charities they waive the fee's then cross charge them to the smaller customers... because politically it's easier to say that you support charities, you collected all the money for comic relief and did it all with a charitable spirit costing the charity nothing... then don't say that you just charged a smaller charity more because of that.
that's why comic relief get charged nothing, and a smaller charity are getting charged 10%,
if you consider that a large charity like comic relief is making greater use of the equipment, the large events means that staff are probably working on standby rather than on call through the night (to make sure that the system doesn't fall over) and cost more because of that it seems unfair to not charge them!
If they charged everyone fee's to process their donation -i.e if every charity or organisation were to pay their own way fairly, then the processing fee could probably fall to a much lower percentage anyway... (so 1% of all donations rather than 10% of a tenth of the donations)
and to all the posts above saying it's a charity, I don't do any business with EE, but if I did, why should my service charge go up to support a load of charities whose cause I may not even agree with?