Paypal does seem to be in the position of being the worst choice around, apart from all the others.
I think it's tolerated rather than loved - and barely at that - but for AUK purposes it has the advantage of being well recognised, (reasonably) trusted, and (mostly) just working.
It's caused problems for organisers a few times, but despite this I think it's currently mostly adequate - and of course, it's fairly well embedded.
We're certainly keeping an eye on other options: inevitably though, when there's an alternative available that's better/cheaper/more reliable/as trusted/as well known, that'll only be the start of persuading 200-odd organisers to sign up to the new super service ...
PayPal already have in their terms and conditions that you can't charge a different price to other payment methods. We came across that when setting up the LEL Shop for the merchandise.
I suspect that's not proactively enforced though, only in response to complaints (at any rate for low cost transactions). And at least organisers can say that cheques only pay for the entry, while Paypal receipts are for the entry plus stamps and envelopes.