Literally every other computer came with serial and parallel ports, when the iMac came out. Yet we’re better off now for Apple having dropped them. Citing, “but we’ve always done it this way and everyone else is still doing it that way” is not compelling evidence in favor of continuing to do it that way. Otherwise we wouldn't have cars, or computers, or smartphones, or modern medicine.
You’re looking at it as a “free prize” (it was never free) that you’re no longer getting, so you’re unhappy because you feel like you’ve lost something. I see unused Apple chargers and cables sitting in a drawer (and I know other people who have the same experience, it’s not just me), and I see needless waste, and that makes me unhappy.
It’s not like you get iPhones out of a vending machine, you have to order them, whether in the store or online, and you already have to specify a lot of choices in the process - size, color, storage capacity, etc. I think it’s a great idea to have the questions include “do you need a charger and/or headphones” in addition to all those other questions. An argument could be made for, if you’re ordering the charger or earphones at the same time, add some sort of bundling discount. But that’s a business/marketing question, not a moral one. They can choose the path they think makes both them and the customers most happy.