One would not need YC for many of the things YC supports, but the mentoring, dinners, intensity, those things help deliver and make a success.
And I have operated a 10% on net earnings since forever. Well, since I learned about them at school... from a Sikh friend. It's called Dasvandh in Sikhism, and is literally 10% and must go to community. Islam has the Zakat, Christianity the Tithe, and atheists just give (though there isn't as widespread awareness in predominantly non-religious countries of the habit).
I choose to give to a variety of charities, but things like Open Rights, MSF, Computers for Africa, etc win out. And of course I consider open source donations and contributions to be within this.
Mostly... it's static, and one just needs accounting tools. But sometimes it varies by demand, i.e. Open Street Map request recently, or perhaps a humanitarian crisis.
Giving individually, direct, makes it hard to make adjustments as a reaction to urgent things like that. One cannot just cancel and renew standing orders easily, most charities wish to own the whole thing (naturally, as they want to have a base revenue guaranteed), but this actually makes it harder for donors to give more at times and makes it harder for donors to give more regularly (if they may need to make adjustments).
5% is too much, I'd probably suggest barely 1% on the payment processing. Instead it's services to charities that would produce the revenue, and fees to donors when you help get their tax return sorted, after all you would know that you helped them claim back a certain figure. There's obviously a lot of money there, but the business model would have to be worked on to make sure it didn't discourage giving.