Yes, it's justifiable.
Larger donations have a higher risk of fraud and chargebacks, so on average it will cost Patreon more to handle this. Additionally, it's not uncommon for credit card companies to charge a fee, even if Patreon wins the chargeback request. If a user donates $10 to a specific creator and initiates a chargeback, who should end up paying the chargeback fee and the donation amount (if the chargeback is successfull?)
You can't charge the user who initiated the chargeback, especially if they were successful. The only thing you can really do is ban them from the service in the future. So, do you take those fees from the creators who received the donation, or do you spread the cost among other creators/donors?
You can't realistically charge the donors. If I were to go to Patreon to try and give someone $5 but was told, thanks for donating, but we're going to charge you an extra $2 because that's the average cost per donor to provide the service, develop new products, advertise, etc., I'm not going to donate. Most people won't.
So do you charge the creators? Let's say the cost per creator is $20/month. If a creator only earns $10, do they then actually owe $10? What creator is going to use the service if they might end up owing money?
The answer, of course, is you figure out the average percentage of a transaction you need to take. You do this because it provides both donors and creators clear information on how much money goes to the creator, what goes to the payment processor/credit card provider, and what percentage goes to Patreon.
But I mean, if you really think that's not a good justification, why not start your own competing option with a business model you think is more fair.