The amount of indicator is so small that you don't consider it. It's a weaker acid than what you are titrating, so the proton of the indicator doesn't matter until the weak acid you're titrating has been fully deprotonated, which is the equivalence point you are looking for. Think of it like a diprotic acid. The second proton has no affect until you have removed the first one. The indicator's proton doesn't matter until the weak acid's proton is gone.